Photoreceptor rescue by an abbreviated human RPGR gene in a murine model of X-linked retinitis pigmentosa.

The X-linked RP3 gene codes for the ciliary protein RPGR and accounts for over 10% of inherited retinal degenerations. The critical RPGR-ORF15 splice variant contains a highly repetitive purine-rich linker region that renders it unstable and difficult to adapt for gene therapy. To test the hypothesis that the precise length of the linker region is not critical for function, we evaluated whether adeno-associated virus-mediated replacement gene therapy with a human ORF15 variant containing in-frame shortening of the linker region could reconstitute RPGR function in vivo. We delivered human RPGR-ORF15 replacement genes with deletion of most (314 codons, 'short form') or 1/3 (126 codons, 'long form') of the linker region to Rpgr null mice. Human RPGR-ORF15 expression was detected post treatment with both forms of ORF15 transgenes. However, only the long form correctly localized to the connecting cilia and led to significant functional and morphological rescue of rods and cones. Thus the highly repetitive region of RPGR is functionally important but that moderate shortening of its length, which confers the advantage of added stability, preserves its function. These findings provide a theoretical basis for optimizing replacement gene design in clinical trials for X-linked RP3.

Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations.

Single single-nucleotide polymorphism (SNP) genome-wide association studies (SSGWAS) may fail to identify loci with modest effects on a trait. The recently developed regional heritability mapping (RHM) method can potentially identify such loci. In this study, RHM was compared with the SSGWAS for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG)). Data comprised 2246 adults from isolated populations genotyped using ∼300 000 SNP arrays. The results were compared with large meta-analyses of these traits for validation. Using RHM, two significant regions affecting HDL on chromosomes 15 and 16 and one affecting LDL on chromosome 19 were identified. These regions covered the most significant SNPs associated with HDL and LDL from the meta-analysis. The chromosome 19 region was identified in our data despite the fact that the most significant SNP in the meta-analysis (or any SNP tagging it) was not genotyped in our SNP array. The SSGWAS identified one SNP associated with HDL on chromosome 16 (the top meta-analysis SNP) and one on chromosome 10 (not reported by RHM or in the meta-analysis and hence possibly a false positive association). The results further confirm that RHM can have better power than SSGWAS in detecting causal regions including regions containing crucial ungenotyped variants. This study suggests that RHM can be a useful tool to explain some of the 'missing heritability' of complex trait variation.

First Report of Stem Blight of Blueberry in California Caused by Neofusicoccum parvum.

In July 2013 in coastal (Santa Barbara County) California, commercial plantings of southern highbush blueberry (Vaccinium corymbosum) developed symptoms of a previously undiagnosed disease. Symptoms consisted of reddening and wilting of foliage, with leaves and small twigs later drying up. The bark of diseased branches was discolored and sunken; removal of this bark revealed a brown discoloration of the underlying wood. Approximately 5% of the planting was affected. When placed on acidified potato dextrose agar (A-PDA), surface disinfested pieces of symptomatic wood consistently yielded one type of fungus. On A-PDA, isolates produced extensive white aerial mycelium that turned dark gray after 4 to 5 days and formed pycnidia after 21 days. Three single-spore isolates were grown on PDA for 21 days for morphological and molecular characterization. Conidia were hyaline, smooth, and ellipsoid with round apices and truncated bases. Conidia measured 13 to 20 × 5 to 7.5 µm (n = 50; mean 16.7 × 6.1 µm), with a length/width ratio of 2.73. After 25 days, conidia became biseptate with a darker middle cell. rDNA sequences of the internal transcribed spacer (ITS) region of the isolates (GenBank KJ126847 to 49), amplified using primers ITS1 and ITS4 (5), were 99% identical to the holotype isolate of Neofusicoccum parvum Pennycook and Samuels (3) by a BLAST query (GU251125). Partial sequences of the translation elongation factor 1-alpha (EF1-α) gene (KJ126850 to 52), obtained using primers EF728Fa and EF986R (5), were 99% identical to N. parvum (GU251257). To demonstrate Koch's postulates, 14-day-old colonies of the three N. parvum isolates were grown on A-PDA. Using three blueberry cultivars (Abundance, Jewel, and Snowchaser), slits were cut beneath the epidermis of branches 1 cm diameter or less; one colonized agar plug (6 mm diameter) was placed into each cut and the epidermis was resealed with Parafilm. Ten inoculations (one inoculation per branch; two branches per plant) were made for each isolate and each cultivar; inoculated plants were maintained in a greenhouse. After 10 to 14 days, leaves on inoculated branches turned red and wilted, bark above and below the inoculation sites turned brown, and vascular tissue beneath the bark was also brown. After 21 days, diseased areas became sunken. N. parvum was recovered from all inoculated branches of all cultivars and matched the characteristics of the original isolates. Control branches, inoculated with sterile agar plugs, did not develop any symptoms and N. parvum was not isolated. This experiment was repeated with similar results. Many Botryosphaeriaceae species, including N. parvum, are associated with canker and dieback symptoms on blueberry worldwide (2). To our knowledge, this is the first documentation of stem blight caused by N. parvum on blueberry in CA. Blueberry is a rapidly expanding industry in the state, with 960 ha planted in 2005 increasing to 2,830 ha in 2012 (1). Drought stress predisposes plants to stem blight caused by Botryosphaeriacease species (4); therefore, expansion into arid areas of CA could increase the incidence and severity of N. parvum. References: (1) N. Amer. Blueberry Council. 2012 World Blueberry Acreage & Prod. Rept., 2013. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab., online publication, ARS, USDA. Retrieved February 5, 2014. (3) S. R Pennycook and G. J. Samuels. Mycotaxon 24:445, 1985. (4) W. A. Sinclair and H. H. Lyon. Diseases of Trees and Shrubs, Second Edition. Comstock Publ. Assoc. 2005. (5) B. Slippers et al. Mycologia 96:83, 2004.

Population choice in mapping genes for complex diseases.

The difficulty of identifying susceptibility genes for common diseases has polarized geneticists' views on what disease models are appropriate and how best to proceed once high-density genome maps become available. Different disease models have different implications for using linkage or linkage-disequilibrium-based approaches for mapping complex disease genes. We argue that the choice of study population is a critical factor when designing a study, and that genetically simplified isolates are more useful than diverse continental populations under most assumptions.

Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa.

The gene RPGR was previously identified in the RP3 region of Xp21.1 and shown to be mutated in 10-20% of patients with the progressive retinal degeneration X-linked retinitis pigmentosa (XLRP). The mutations predominantly affected a domain homologous to RCC1, a guanine nucleotide exchange factor for the small GTPase Ran, although they were present in fewer than the 70-75% of XLRP patients predicted from linkage studies. Mutations in the RP2 locus at Xp11.3 were found in a further 10-20% of XLRP patients, as predicted from linkage studies. Because the mutations in the remainder of the XLRP patients may reside in undiscovered exons of RPGR, we sequenced a 172-kb region containing the entire gene. Analysis of the sequence disclosed a new 3' terminal exon that was mutated in 60% of XLRP patients examined. This exon encodes 567 amino acids, with a repetitive domain rich in glutamic acid residues. The sequence is conserved in the mouse, bovine and Fugu rubripes genes. It is preferentially expressed in mouse and bovine retina, further supporting its importance for retinal function. Our results suggest that mutations in RPGR are the only cause of RP3 type XLRP and account for the disease in over 70% of XLRP patients and an estimated 11% of all retinitis pigmentosa patients.

A locus for bipolar affective disorder on chromosome 4p.

The main clinical feature of bipolar affective disorder is a change of mood to depression or elation. Unipolar disorder, also termed major depressive disorder, describes the occurrence of depression alone without episodes of elevated mood. Little is understood about the underlying causes of these common and severe illnesses which have estimated lifetime prevalences in the region of 0.8% for bipolar and 6% for unipolar disorder. Strong support for a genetic aetiology is found in the familial nature of the condition, the increased concordance of monozygotic over dizygotic twins and adoption studies showing increased rates of illness in children of affected parents. However, linkage studies have met with mixed success. An initial report of linkage on the short arm of chromosome 11 (ref. 4) was revised and remains unreplicated. Reports proposing cosegregation of genes found on the X chromosome with bipolar illness have not been supported by others. More recently bipolar disorder has been reported to be linked with markers on chromosomes 18, 21, 16 and a region on the X chromosome different from those previously suggested. We have carried out a linkage study in twelve bipolar families. In a single family a genome search employing 193 markers indicated linkage on chromosome 4p where the marker D4S394 generated a two-point lod score of 4.1 under a dominant model of inheritance. Three point analyses with neighbouring markers gave a maximum lod score of 4.8. Eleven other bipolar families were typed using D4S394 and in all families combined there was evidence of linkage with heterogeneity with a maximum two-point lod score of 4.1 (theta = 0, alpha = 0.35).

Identification of the gene that, when mutated, causes the human obesity syndrome BBS4.

Bardet-Biedl syndrome (BBS, MIM 209900) is a heterogeneous autosomal recessive disorder characterized by obesity, pigmentary retinopathy, polydactyly, renal malformations, mental retardation, and hypogenitalism. The disorder is also associated with diabetes mellitus, hypertension, and congenital heart disease. Six distinct BBS loci map to 11q13 (BBS1), 16q21 (BBS2), 3p13-p12 (BBS3), 15q22.3-q23 (BBS4), 2q31 (BBS5), and 20p12 (BBS6). Although BBS is rare in the general population (<1/100,000), there is considerable interest in identifying the genes causing BBS because components of the phenotype, such as obesity and diabetes, are common. We and others have demonstrated that BBS6 is caused by mutations in the gene MKKS (refs. 12,13), mutation of which also causes McKusick-Kaufman syndrome (hydrometrocolpos, post-axial polydactyly, and congenital heart defects). MKKS has sequence homology to the alpha subunit of a prokaryotic chaperonin in the thermosome Thermoplasma acidophilum. We recently identified a novel gene that causes BBS2. The BBS2 protein has no significant similarity to other chaperonins or known proteins. Here we report the positional cloning and identification of mutations in BBS patients in a novel gene designated BBS4.

Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate.

Hereditary human retinal degenerative diseases usually affect the mature photoreceptor topography by reducing the number of cells through apoptosis, resulting in loss of visual function. Only one inherited retinal disease, the enhanced S-cone syndrome (ESCS), manifests a gain in function of photoreceptors. ESCS is an autosomal recessive retinopathy in which patients have an increased sensitivity to blue light; perception of blue light is mediated by what is normally the least populous cone photoreceptor subtype, the S (short wavelength, blue) cones. People with ESCS also suffer visual loss, with night blindness occurring from early in life, varying degrees of L (long, red)- and M (middle, green)-cone vision, and retinal degeneration. The altered ratio of S- to L/M-cone photoreceptor sensitivity in ESCS may be due to abnormal cone cell fate determination during retinal development. In 94% of a cohort of ESCS probands we found mutations in NR2E3 (also known as PNR), which encodes a retinal nuclear receptor recently discovered to be a ligand-dependent transcription factor. Expression of NR2E3 was limited to the outer nuclear layer of the human retina. Our results suggest that NR2E3 has a role in determining photoreceptor phenotype during human retinogenesis.

SNP mistyping in genotyping arrays--an important cause of spurious association in case-control studies.

Using genome-wide association studies to identify genetic variants contributing to disease has been highly successful with many novel genetic predispositions identified and biological pathways revealed. Several pitfalls for spurious association or non-replication have been highlighted: from population structure, automated genotype scoring for cases and controls, to age-varying association. We describe an important yet unreported source of bias in case-control studies due to variations in chip technology between different commercial array releases. As cases are commonly genotyped with newer arrays and freely available control resources are frequently used for comparison, there exists an important potential for false associations which are robust to standard quality control and replication design.

Multi-system neurological disease is common in patients with OPA1 mutations.

Additional neurological features have recently been described in seven families transmitting pathogenic mutations in OPA1, the most common cause of autosomal dominant optic atrophy. However, the frequency of these syndromal 'dominant optic atrophy plus' variants and the extent of neurological involvement have not been established. In this large multi-centre study of 104 patients from 45 independent families, including 60 new cases, we show that extra-ocular neurological complications are common in OPA1 disease, and affect up to 20% of all mutational carriers. Bilateral sensorineural deafness beginning in late childhood and early adulthood was a prominent manifestation, followed by a combination of ataxia, myopathy, peripheral neuropathy and progressive external ophthalmoplegia from the third decade of life onwards. We also identified novel clinical presentations with spastic paraparesis mimicking hereditary spastic paraplegia, and a multiple sclerosis-like illness. In contrast to initial reports, multi-system neurological disease was associated with all mutational subtypes, although there was an increased risk with missense mutations [odds ratio = 3.06, 95% confidence interval = 1.44-6.49; P = 0.0027], and mutations located within the guanosine triphosphate-ase region (odds ratio = 2.29, 95% confidence interval = 1.08-4.82; P = 0.0271). Histochemical and molecular characterization of skeletal muscle biopsies revealed the presence of cytochrome c oxidase-deficient fibres and multiple mitochondrial DNA deletions in the majority of patients harbouring OPA1 mutations, even in those with isolated optic nerve involvement. However, the cytochrome c oxidase-deficient load was over four times higher in the dominant optic atrophy + group compared to the pure optic neuropathy group, implicating a causal role for these secondary mitochondrial DNA defects in disease pathophysiology. Individuals with dominant optic atrophy plus phenotypes also had significantly worse visual outcomes, and careful surveillance is therefore mandatory to optimize the detection and management of neurological disability in a group of patients who already have significant visual impairment.

Identification of Species in the Botryosphaeriaceae Family Causing Stem Blight on Southern Highbush Blueberry in Florida.

Stem blight of southern highbush blueberry (SHB) results in premature plant mortality and has been identified by Florida blueberry growers as the economically most important disease for the industry. In 2007, plants with stem blight and dieback symptoms were sampled at 4-month intervals from two farms located in Alachua and Polk Co., FL. In all, 30 cane samples (stem blight) and 30 crown segments (dieback) were collected at each sample date and each location. In total, 360 samples were collected; fungal species in the family Botryosphaeriaceae were isolated from 85% of the samples. Based on morphology and phylogenetic analysis of the internal transcribed spacer region and elongation factor 1-α (EF1-α) sequences, two dominant species recovered from SHB in Florida were identified: Lasiodiplodia theobromae and Neofusicoccum ribis. Species isolation was independent of location, symptom type, and time of year. Additional samplings are needed to investigate population change over multiple years and in the rest of the southeastern United States. Breeding for resistance and management of stem blight and dieback in Florida should focus on these two fungal species.

First Report of Lasiodiplodia theobromae Associated with Stem Blight of Southern Highbush Blueberries in Florida.

Stem blight of southern highbush blueberries has been attributed to Botryosphaeria dothidea (2). Symptoms include necrotic branches with attached leaves and brown discoloration of the vasculature extending the length of the affected branch. A 2007 field survey of stem blight in Florida resulted in isolates of the previously reported B. dothidea and Neofusicoccum ribis and isolates of unreported Lasiodiplodia theobromae (2). Isolates of L. theobromae were identified to species level by morphological characterization (3). Identity was confirmed by comparison of rDNA sequences of representative isolates (GenBank Accession No. FJ882072) to reference sequences (99% similarity to Accession No. EF622074) (1). Seven, fresh, pruning wounds on southern highbush blueberries cv. Misty were inoculated with a 10-mm V8 juice agar plug of isolate MixFC-6 taken from the margin of a 3-day-old colony. Seven wounds were inoculated with a sterile agar plug. All plugs were attached to the wounds with Parafilm. Mean lesion length 14 days after inoculation was 8.6 ± 2.4 cm. The pathogen was reisolated from the margin of lesions and identified by colony growth characteristics on potato dextrose agar. No lesions were observed on control plants. To our knowledge, this is the first report that stem blight of southern highbush blueberries in Florida can be caused by L. theobromae. References: (1) A. Alves et al. Fungal Divers. 28:1, 2008. (2) F. L. Caruso and D. C. Ramsdell. Compendium of Blueberry and Cranberry Diseases. The American Phytopathological Society, St. Paul, MN, 1995. (3) P. W. Crous et al. Stud. Mycol. 55:235, 2006.

Cancer risk in patients with constitutional chromosome deletions: a nationwide British cohort study.

The finding of increased risks of specific cancers in individuals with constitutional deletions of chromosomes 11p and 13q led to the discovery of cancer predisposition genes at these locations, but there have been no systematic studies of cancer risks in patients with constitutional deletions, across the chromosome complement. Therefore, we assessed cancer incidence in comparison with national cancer incidence rates in a follow-up of 2561 patients with constitutional autosomal chromosome deletions diagnosed by microscopy or fluorescence in situ hybridisation in Britain during the period 1965-2002. Thirty cancers other than non-melanoma skin cancer occurred in the cohort (standardised incidence ratio (SIR)=2.4, 95% confidence interval (CI) 1.6-3.5). There were significantly increased risks of renal cancer in persons with 11p deletions (SIR=1869, 95% CI 751-3850; P=4 x 10(-21)), eye cancer with 13q deletions (SIR=1084, 95% CI 295-2775; P=2 x 10(-11)), and anogenital cancer with 11q deletions (SIR=305, 95% CI 63-890; P=3 x 10(-7)); all the three latter cancers were in the 11 subjects with 11q24 deletions. The results strongly suggest that in addition to suppressor genes relating to Wilms' tumour risk on 11p and retinoblastoma on 13q, there are suppressor genes around 11q24 that greatly affect anogenital cancer risk.

New insights into genetic eye disease.

Most human genetic abnormalities affecting the eye are clinically detectable but, until recently, our knowledge of the genes concerned was sparse. Several genes capable of causing progressive degeneration of the mammalian retina have now been identified by a combination of 'positional cloning' and 'candidate gene' approaches. One of these genes codes for the visual pigment rhodopsin. The identification of two genes (rd and rds) capable of causing retinal degeneration in the mouse has provided candidate genes for similar human disorders.

The optimized effective potential with finite temperature.

The optimized effective potential (OEP) method provides an additional level of exactness in the computation of electronic structures, e.g. the exact exchange energy can be used. This extra freedom is likely to be important in moving density functional methods beyond traditional approximations such as the local density approximation. We provide a new density-matrix-based derivation of the gradient of the Kohn-Sham energy with respect to the effective potential. This gradient can be used to iteratively minimize the energy in order to find the OEP. Previous work has indicated how this can be done in the zero temperature limit. This paper generalizes the previous results to the finite temperature regime. Equating our gradient to zero gives a finite temperature version of the OEP equation.

In vitro and in vivo antitumor activity of ZENECA ZD0490, a recombinant ricin A-chain immunotoxin for the treatment of colorectal cancer.

ZENECA ZD0490 is a recombinant ricin A-chain-containing immunotoxin that recognizes an antigen that is expressed on approximately 65% of colorectal tumors. The antigen CA242 is recognized by a mouse monoclonal antibody designated C242. C242 antibody was conjugated to recombinant ricin A-chain via a methyl-hindred disulfide linker which confers in vivo stability. ZD0490 was extremely potent against colorectal cell lines CoLo201 and CoLo205, which express the CA242 antigen. ZD0490 activity was determined in vitro by both protein synthesis inhibition (50% inhibitory concentrations of 1-20 ng/ml after 24-h exposure) and clonogenic assay (76-95% cell kill after 24-h exposure to a 50% inhibitory concentration for protein synthesis inhibition; > 99.99% cell kill at 1000 ng/ml). This in vitro activity was translated to in vivo efficacy where single dose i.v. administration of 2.5 mg/kg of ZD0490 was sufficient to induce substantial growth delays of both CoLo201 and CoLo205 s.c. tumors in nude mice. This growth delay equates to between 40 and 60% inhibition of tumor protein synthesis as quantified by an in vivo [14C]leucine incorporation assay. Using this technique, it was shown that protein synthesis inhibition persisted for at least 96 h after a single dose of ZD0490. Administration of the same total dose given as daily doses over 5 days did not alter the antitumor efficacy of ZD0490 in either the growth delay or the protein synthesis inhibition assays. The in vitro and in vivo activity of ZD0490 detailed in this paper show that this novel immunotoxin is worthy of clinical evaluation, which is currently under way in the United Kingdom.

ZD2767, an improved system for antibody-directed enzyme prodrug therapy that results in tumor regressions in colorectal tumor xenografts.

ZD2767 represents an improved version of antibody-directed enzyme prodrug therapy. It consists of a conjugate of the F(ab')2 A5B7 antibody fragment and carboxypeptidase G2 (CPG2) and a prodrug, 4-[N,N-bis(2-iodoethyl)amino]phenoxycarbonyl L-glutamic acid. The IC50 of the prodrug against LoVo colorectal tumor cells was 47 microM, and cleavage by CPG2 released the potent bis-iodo phenol mustard drug (IC50 = 0.34 microM). The drug killed both proliferating and quiescent LoVo cells. Administration of the ZD2767 conjugate to nude mice bearing LoVo colorectal xenografts resulted in approximately 1% of injected ZD2767 conjugate localizing/g of tumor after 72 h, and blood and normal tissue levels of the conjugate were 10-50-fold lower. A single round of therapy involving the administration of the prodrug 72 h after the conjugate to athymic mice bearing established LoVo xenografts resulted in approximately 50% of the tumors undergoing complete regressions, tumor growth delays greater than 30 days, and little toxicity (as judged by body-weight loss). Similar studies using a control antibody-CPG2 conjugate that does not bind to LoVo tumor cells resulted in a growth delay of less than 5 days, confirming the tumor specificity of this approach. These studies demonstrate the potential of ZD2767 for the treatment of colorectal cancer.