Making an impression on X-linked mental retardation

Oligophrenin-1 encodes a rhoGAP protein involved in X-linked mental retardationBilluart, P. (1998)Nature 392, 923–926PAK3 mutation in nonsyndromic X-linked mental retardationAllen, K.M. et al. (1998)Nat. Genet. 20, 25–30Mutations in GDI1 are responsible for X-linked non-specific mental retardationD'Adamo, P. et al. (1998)Nat. Genet. 19, 134–139Non-specific X-linked semidominant mental retardation by mutations in a Rab GDP-dissociation inhibitorBienvenu, T. et al. (1998)Hum. Mol. Genet. 7, 1311–1315     

Non-viral gene transfer: liposomes and nanospheres promise to deliver the goods

Effective treatment of early endobronchial cancer with regional administration of liposome–p53 complexesZou, Y. et al. (1998)J. Natl. Cancer Inst. 90, 1130–1137Controlled gene delivery by DNA–gelatin nanospheresTruong-Le, V.L. et al. (1998)Hum. Gene Ther. 9, 1709–1717     

TP53 on trial for cancer gene therapy

Adenovirus-mediated p53 gene transfer in patients with advanced recurrent head and neck squamous cell carcinomaClayman G.L. et al. (1998)J. Clin. Oncol. 16, 2221–2232Gene therapy for non-small cell lung cancer: a preliminary report of a phase I trial of adenoviral p53 gene replacementRoth, J.A. et al. (1998)Semin. Oncol. 25, 33–37     

Borna disease virus takes the acid test

Mechanism of Borna disease virus entry into cellsGonzalez-Dunia, D. et al. (1998)J. Virol. 72, 783–788     

Better mutation detection

Mutation detection and typing of polymorphic loci through double-strand conformation analysisArgüello, J.R. et al. (1998)Nat. Genet. 18, 192–194     

Increasing the options for inflammatory bowel disease treatment?

Curative treatment of an experimentally induced colitis by a CD44 variant V7-specific antibodyWittig, B. et al. (1998)J. Immunol. 161, 1069–1073     

Electronic zoo blotting identifies a modifier gene for spinal muscular atrophy

Identification of a candidate modifying gene for spinal muscular atrophy by comparative genomicsScharf, J.M. et al. (1998)Nat. Genet. 20, 83–86     

Unusual imprinting defects with low recurrence risks

Sporadic imprinting defects in Prader–Willi syndrome and Angelman syndrome: implications for imprint-switch models, genetic counselling, and prenatal diagnosisBuiting, K. et al. (1998)Am. J. Hum. Genet. 63, 170–180     

Crosstalk among cancer signalling pathways

Identification of c-MYC as a target of the APC pathwayHe, T-C. et al. (1998)Science 281, 1509–1512Smad3 mutant mice develop metastatic colorectal cancerZhu, Y. et al. (1998)Cell 94, 703–714     

Aspirin as a cancer-preventing drug

Aspirin suppresses the mutator phenotype associated with hereditary nonpolyposis colorectal cancer by genetic selectionRuschoff, J. et al. (1998)Proc. Natl. Acad. Sci. U. S. A. 95, 11301–11306     

Baldness as a mendelian genetic trait

Alopecia universalis associated with a mutation in the human hairless geneAhmad, W. et al. (1998)Science 279, 720–724     

Systematic synthesis of nonviral gene therapy vectors

Lipitoids—novel cationic lipids for cellular delivery of plasmid DNA in vitroHuang, C-Y. et al. (1998)Chem. Biol. 5, 345–354     

Uric acid might herald new hopes for multiple sclerosis patients

Uric acid: a natural scavenger of peroxynitrite, in experimental allergic encephalomyelitis and multiple sclerosisHooper, D.C. et al. (1998)Proc. Natl. Acad. Sci. U. S. A. 95, 675–680     

In Planta Mutagenesis Determines the Functional Regions of the Wheat Puroindoline Proteins

In planta analysis of protein function in a crop plant could lead to improvements in understanding protein structure/function relationships as well as selective agronomic or end product quality improvements. The requirements for successful in planta analysis are a high mutation rate, an efficient screening method, and a trait with high heritability. Two ideal targets for functional analysis are the Puroindoline a and Puroindoline b (Pina and Pinb, respectively) genes, which together compose the wheat (Triticum aestivum L.) Ha locus that controls grain texture and many wheat end-use properties. Puroindolines (PINs) together impart soft texture, and mutations in either PIN result in hard seed texture. Studies of the PINs'' mode of action are limited by low allelic variation. To create new Pin alleles and identify critical function-determining regions, Pin point mutations were created in planta via EMS treatment of a soft wheat. Grain hardness of 46 unique PIN missense alleles was then measured using segregating F₂:F₃ populations. The impact of individual missense alleles upon PIN function, as measured by grain hardness, ranged from neutral (74%) to intermediate to function abolishing. The percentage of function-abolishing mutations among mutations occurring in both PINA and PINB was higher for PINB, indicating that PINB is more critical to overall Ha function. This is contrary to expectations in that PINB is not as well conserved as PINA. All function-abolishing mutations resulted from structure-disrupting mutations or from missense mutations occurring near the Tryptophan-rich region. This study demonstrates the feasibility of in planta functional analysis of wheat proteins and that the Tryptophan-rich region is the most important region of both PINA and PINB.NATURAL selection has captured a relatively small subset of potentially useful protein sequences. Unraveling the critical features of proteins via understanding the process of their evolution is a powerful approach for proteins present in many diverse species (Bashford et al. 1987; Hampsey et al. 1988). However, this approach is not feasible for the wheat puroindolines (PINs) that are present only in hexaploid wheat and related species (Massa and Morris 2006). The PINs are unique in structure in having a tryptophan-rich domain and are members of the protease inhibitor/seed storage/lipid transfer protein family (PF00234) (Finn et al. 2008).The tryptophan-rich domain has been hypothesized to control PIN function (Giroux and Morris 1997), but there is no unbiased direct evidence for this since previous studies have focused on the tryptophan box alone (Evrard et al. 2008). A nonbiased approach would consist of random mutagenesis followed by functional analysis (Bowie et al. 1990). This approach has been used extensively for proteins that can be expressed in vitro using either random (Tarun et al. 1998; Guo et al. 2004; Smith and Raines 2006; Georgelis et al. 2007) or site-directed mutations (Miyahara et al. 2008; Osmani et al. 2008). However, functional analysis of many plant proteins in vitro may not be comparable to in planta analysis. In the case of puroindolines, there is no in vitro assay that properly mimics the synergistic binding of PINA and PINB to starch granules or is as easy to measure as grain hardness. Therefore, creation and analysis of a large number of new alleles in wheat in planta is an ideal approach to dissect PIN function.The absence of high-throughput transformation and/or functional screening methods in most crop plants is the largest obstacle in the way of in planta protein functional analysis. However, high-throughput in vitro random or targeted mutagenesis followed by functional analysis has been demonstrated in Arabidopsis thaliana (Dunning et al. 2007) and Nicotiana benthamiana (Boter et al. 2007). Traditional in planta mutagenesis followed by analysis of loss-of-function mutations has been used to clone unknown genes (Xiong et al. 2001) or to define function for candidate genes (Haralampidis et al. 2001; Qi et al. 2006). A high-throughput in planta functional approach for PINA and PINB seems attractive for three reasons. First, the EMS mutation rate in wheat is higher than in any other plant (Slade et al. 2005; Feiz et al. 2009a). Second, PINs control the vast majority of variation in grain hardness (Campbell et al. 1999). Finally, a small-scale preliminary study indicated the feasibility of this approach (Feiz et al. 2009a).PINA and PINB are cysteine-rich proteins unique in having a tryptophan-rich domain (Blochet et al. 1993) and together compose the wheat Hardness (Ha) locus (Giroux and Morris 1998; Wanjugi et al. 2007a). Ha is located on chromosome 5DS and is the major determinant of wheat endosperm texture (Mattern et al. 1973; Law et al. 1978; Campbell et al. 1999). Soft texture (Ha) results when both Pin genes are wild type (Pina-D1a, Pinb-D1a) while hard texture (ha) results from mutations in either Pin (Giroux and Morris 1997, 1998). Transgenic studies in rice (Krishnamurthy and Giroux 2001), wheat (Beecher et al. 2002; Martin et al. 2006), and corn (Zhang et al. 2009) have demonstrated that Pin mutations are causative to hard grain texture. PINA and PINB are not functionally interchangeable and control grain hardness via cooperative binding to starch granules (Hogg et al. 2004; Swan et al. 2006; Wanjugi et al. 2007a; Feiz et al. 2009b). PIN binding to starch granules is mediated by polar lipids (Greenblatt et al. 1995) and PIN abundance is correlated with seed polar lipid content (Feiz et al. 2009b). Variation in PIN function affects grain hardness along with nearly all end product quality traits (Hogg et al. 2005; Martin et al. 2007, 2008; Wanjugi et al. 2007b; Feiz et al. 2008). Determining PINs'' function-determining regions could lead to greater knowledge of their mode of action and to wheat quality improvements. Current PIN functional analyses have been limited to in vitro tests of binding to each other (Ziemann et al. 2008) or to yeast membranes (Evrard et al. 2008).Here, we report the creation and functional analysis in planta of new alleles of PINA and PINB. This is the first successful in planta functional analysis of a crop plant protein.     

Toxic triplets provide clues to neurodegeneration

Cleavage, aggregation and toxicity of the expanded androgen receptor in spinal and bulbar muscular atrophyMerry, D.E. et al. (1998)Hum. Mol. Genet. 7, 693–701Truncated N-terminal fragments of huntingtin with expanded glutamine repeats form nuclear and cytoplasmic aggregates in cell cultureCooper, J.K. et al. (1998)Hum. Mol. Genet. 7, 783–790Aggregation of N-terminal huntingtin is dependent on the length of its glutamine repeatsLi, S.H. and Li, X.J. (1998)Hum. Mol. Genet. 7, 777–782     

Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16405–16415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93–102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.     

Winning the war against antibiotic resistance

Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-β-lactamaseToney, J.H. et al. (1998)Chem. Biol. 5, 185–196Autoinducer of virulence as a target for vaccine and therapy against Staphylococcus aureusBalaban, N. et al. (1998)Science 280, 438–440     

How to lose resistance to Aspergillus infections

The distinct risk factors to deadly infections by Aspergillus fumigatus (Af) in intensive care unit (ICU) patients are well known; however, so far, the mechanistic link between these predisposing conditions has been unknown. Sarden et al. recently unraveled a shared B1a lymphocyte–natural antibody–neutrophil defense pathway to Af, opening new perspectives in diagnostics and therapeutics.     

pH regulates peptide–receptor perception

Diverse plant small peptides are perceived by their corresponding receptors to mediate local or long-distance intercellular communications in various developmental and adaptive programs; notably, the mechanisms of peptide–receptor perception remain largely unrevealed. Two reports (Liu et al.; Diaz-Ardila et al.) shed light on how pH regulates peptide–receptor perception.     

Attraction and the single cell

Selective expression of the eotaxin receptor CCR3 by human T helper 2 cellsSallusto, F. et al. (1997)Science 277, 2005–2007Functional expression of the eotaxin receptor CCR3 in T lymphocytes co-localising with eosinophilsGerber, B.O. et al. (1997)Curr. Biol. 7, 836–843Differential expression of chemokine receptors and chemotactic responsiveness of type 1 T helper cells (Th1s) and Th2sBonecchi, R. et al. (1998)J. Exp. Med. 187, 129–134CCR5 is characteristic of Th1 lymphocytesLoetscher, M. et al. (1998)Nature 391, 344–345