Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Identification of nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with no evidence of CYP3A4 time-dependent inhibition and improved aqueous solubility

Herein we report the optimization efforts to ameliorate the potent CYP3A4 time-dependent inhibition (TDI) and low aqueous solubility exhibited by a previously identified lead compound from our NAMPT inhibitor program (1, GNE-617). Metabolite identification studies pinpointed the imidazopyridine moiety present in 1 as the likely source of the TDI signal, and replacement with other bicyclic systems was found to reduce or eliminate the TDI finding. A strategy of reducing the number of aromatic rings and/or lowering cLogD7.4 was then employed to significantly improve aqueous solubility. These efforts culminated in the discovery of 42, a compound with no evidence of TDI, improved aqueous solubility, and robust efficacy in tumor xenograft studies.

A second-generation genetic linkage map for bighead carp (Aristichthys nobilis) based on microsatellite markers

Bighead carp (Aristichthys nobilis) is an important aquaculture fish worldwide. Genetic linkage maps for the species were previously reported, but map resolution remained to be improved. In this study, a second-generation genetic linkage map was constructed for bighead carp through a pseudo-testcross strategy using interspecific hybrids between bighead carp and silver carp. Of the 754 microsatellites genotyped in two interspecific mapping families (with 77 progenies for each family), 659 markers were assigned to 24 linkage groups, which were equal to the chromosome numbers of the haploid genome. The consensus map spanned 1917.3 cM covering 92.8% of the estimated bighead carp genome with an average marker interval of 2.9 cM. The length of linkage groups ranged from 52.2 to 133.5 cM with an average of 79.9 cM. The number of markers per linkage group varied from 11 to 55 with an average of 27.5 per linkage group. Normality tests on interval distances of the map showed a non-normal marker distribution; however, significant correlation was found between the length of linkage group and the number of markers below the 0.01 significance level (two-tailed). The length of the female map was 1.12 times that of the male map, and the average recombination ratio of female to male was 1.10:1. Visual inspection showed that distorted markers gathered in some linkage groups and in certain regions of the male and female maps. This well-defined genetic linkage map will provide a basic framework for further genome mapping of quantitative traits, comparative mapping and marker-assisted breeding in bighead carp.

Value of ecosystem hydropower service and its impact on the payment for ecosystem services

Hydropower is an important service provided by ecosystems. We surveyed all the hydropower plants in the Zagunao River Basin, Southwest China. Then, we assessed the hydropower service by using the InVEST (The Integrated Value and Tradeoff of Ecosystem Service Tools) model. Finally, we discussed the impact on ecological compensation. The results showed that: 1) hydropower service value of ecosystems in the Zagunao River Basin is 216.29 Euro/hm(2) on the average, of which the high-value area with more than 475.65 Euro/hm(2) is about 750.37 km(2), accounting for 16.12% of the whole watershed, but it provides 53.47% of the whole watershed service value; 2) ecosystem is an ecological reservoir with a great regulation capacity. Dams cannot completely replace the reservoir water conservation function of ecosystems, and has high economic and environmental costs that must be paid as well. Compensation for water conservation services should become an important basis for ecological compensation of hydropower development. 3) In the current PES cases, the standard of compensation is generally low. Cascade development makes the value of upstream ecosystem services become more prominent, reflecting the differential rent value, and the value of ecosystem services should be based on the distribution of differentiated ecological compensation.

A weight-of-evidence approach to integrate suspended sediment source information

Sediment monitoring, tracing and modelling are widely used to identify suspended sediment sources. Although each method has inherent limitations and uncertainties, their integration provides opportunities to form collective knowledge and encourages robust management strategies. This paper presents a Weight-of-Evidence approach to integrate multiple Lines-of-Evidence for identifying suspended sediment sources. Three sources of evidence were used: i) stream flow and suspended sediment monitoring at river gauges; ii) geochemical sediment tracing at river junctions; and iii) catchment-scale suspended sediment modelling of hillslope, gully, streambank and unsealed road erosion. We applied this approach on two data-poor catchments in Australia. Some reaches were consistently identified as major sources of sediment from all Lines-of-Evidence. However, inconsistencies between the types of evidence in other areas highlighted the high uncertainty in identifying suspended sediment sources in these areas and the need for further investigation. The integration framework maximised the use of scarce information, enabled explicit consideration of uncertainties for catchment management and identified where future monitoring and research should be targeted.

Tracking chromosome evolution in southern African gerbils using flow-sorted chromosome paints

Desmodillus and Gerbilliscus (formerly Tatera) comprise a monophyletic group of gerbils (subfamily Gerbillinae) which last shared an ancestor approximately 8 million years ago; diploid chromosome number variation among the species ranges from 2n = 36 to 2n = 50. In an attempt to shed more light on chromosome evolution and speciation in these rodents, we compared the karyotypes of 7 species, representing 3 genera, based on homology data revealed by chromosome painting with probes derived from flow-sorted chromosomes of the hairy footed gerbil, Gerbillurus paeba (2n = 36). The fluorescent in situ hybridization data revealed remarkable genome conservation: these species share a high proportion of conserved chromosomes, and differences are due to 10 Robertsonian (Rb) rearrangements (3 autapomorphies, 3 synapomorphies and 4 hemiplasies/homoplasies). Our data suggest that chromosome evolution in Desmodillus occurred at a rate of ~1.25 rearrangements per million years (Myr), and that the rate among Gerbilliscus over a time period spanning 8 Myr is also ~1.25 rearrangements/Myr. The recently diverged Gerbillurus (G. tytonis and G. paeba) share an identical karyotype, while Gerbilliscus kempi, G. afra and G. leucogaster differ by 6 Rb rearrangements (a rate of ~1 rearrangement/Myr). Thus, our data suggests a very slow rate of chromosomal evolution in Southern African gerbils.

Mesenchymal stem cells modified to express interferon-β inhibit the growth of prostate cancer in a mouse model

OBJECTIVE

This study investigated use of mesenchymal stem cells (MSCs) genetically engineered to produce interferon-β (IFN-β) as a gene delivery system to treat prostate cancer in an animal model.

METHODS

To measure the effects on tumour cell growth in vitro, IFN-β-producing MSCs (IFN-β-MSCs) were co-cultured with the prostate cancer cell line PC-3. The in vivo migration of intravenously injected fluorescently-labelled MSCs to healthy tissues and PC-3 xenograft tumours grown in immuno-deficient mice was determined by fluorescence microscopy. The antitumour effects of intravenously injected IFN-β-MSCs on PC-3 xenograft growth and animal survival were also investigated.

RESULTS

IFN-β-MSCs inhibited the growth of PC-3 cells in vitro. Fluorescently-labelled MSCs migrated to the margins and centre of tumour masses but not into healthy tissues. Intravenously injected IFN-β-MSCs significantly reduced PC-3 xenograft tumour weight and increased animal survival compared with controls.

CONCLUSIONS

Intravenously injected IFN-β-MSCs inhibited PC-3 xenograft growth. This could be an effective gene delivery system for treatment of solid human tumours.

First Report of Fusarium pseudograminearum Causing Crown Rot of Wheat in Henan, China

Fusarium pseudograminearum (O'Donnell & Aoki), a residue-borne pathogen, is responsible for crown rot of wheat (Triticum aestivum L.). Since its first detection in Queensland, Australia in 1951, it has been reported in many other countries, but not China (2). In May 2011, a crown rot disease was observed in wheat cv. Aikang 58 in a wheat-maize rotation, irrigable and loam field in Henan Province, China. Diseased wheat plants showed honey brown discoloration in the stem bases and whitehead in some plants, which are symptoms of crown rot with about 70% incidence in a surveyed field (2). The pathogen was isolated from diseased stem base on potato dextrose agar (PDA) after being surface-disinfested with 5% NaClO solution for 2 min. Pure cultures were established on carnation leaf agar (CLA) through a single spore technique and identified by morphological and molecular methods according to protocols described previously (1,3,4). Macroconidia of F. pseudograminearum were formed in abundant sporodochia on CLA cultures grown under the BLB light. Macroconidia were usually five septate (about three to seven) and 27 to 91 × 2.7 to 5.5 μm. Colonies grown on PDA from a single conidium in the dark at 25°C had average radial growth rates of ~4.7 to 9.9 mm per day. Colony pigment on PDA grown under light varied from rose to burgundy, while mycelium ranged from rose to yellow white. Two isolates (WZ-8A and WZ-2B) were selected for molecular identification. The translation elongation factor 1-α gene and rDNA ITS gene were amplified by PCR using the specific primers described previously (4). PCR products were sequenced (GenBank Accession Nos. JN862232 to JN862235). Phylogenic analysis of the sequence indicated that the isolates were identified as F. pseudograminearum. The identification was further confirmed by the F. pseudograminearum species-specific PCR primers (Fp1-1: CGGGGTAGTTTCACATTTCCG and Fp1-2: GAGAATGTGATGACGACAATA) (1). The expected PCR products of 520 bp were produced only in F. pseudograminearum. Isolates WZ-2B and WZ-8A were deposited in the Agriculture Culture Collection of China as ACCC38067 and ACCC 38068, respectively. Pathogenicity tests were conducted by inoculating winter wheat cultivar Wenmai 19 with isolates WZ-8A and WZ-2B through soil inoculation. Inoculum was prepared by growing cultures on sterilized wheat bran and chopped wheat-straw (4:1, v/v) after incubation at 25°C for 2 weeks. This inoculum was added to sterilized soil at 1% by volume and no inoculum was added in control treatment. Five seeds were planted in a 15 cm wide pot in a 20 to 25°C greenhouse, with six replications. Seedling death and crown browning occurred in the inoculated wheat plants after 4 weeks with over 90% incidence, while no symptoms developed in the control plants. The fungus was reisolated from inoculated plants, fulfilling Koch's postulates. To our knowledge, this is the first report of F. pseudograminearum causing crown rot of wheat in China. Considering Henan is the largest wheat production province in China with over 5 million hectares planting area, and the soil and climate conditions are suitable for this disease, it will be a important pathogen of wheat in Henan in the future. References: (1) T. Aoki et al. Mycologia 91:597, 1999. (2) L. W. Burgess. Page 271 in: Crown Rot of Wheat: Fusarium. B. A. Summerell et al., eds. APS Press, St. Paul, MN, 2001. (3) R. G. Francis et al. Trans. Brit. Mycol. Soc. 68:421, 1977. (4) J. B. Scott et al. Mycol. Res. 110:1413, 2006.