Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration

RNA exosomes are multi-subunit complexes conserved throughout evolution and are emerging as the major cellular machinery for processing, surveillance and turnover of a diverse spectrum of coding and noncoding RNA substrates essential for viability. By exome sequencing, we discovered recessive mutations in EXOSC3 (encoding exosome component 3) in four siblings with infantile spinal motor neuron disease, cerebellar atrophy, progressive microcephaly and profound global developmental delay, consistent with pontocerebellar hypoplasia type 1 (PCH1; MIM 607596). We identified mutations in EXOSC3 in an additional 8 of 12 families with PCH1. Morpholino knockdown of exosc3 in zebrafish embryos caused embryonic maldevelopment, resulting in small brain size and poor motility, reminiscent of human clinical features, and these defects were largely rescued by co-injection with wild-type but not mutant exosc3 mRNA. These findings represent the first example of an RNA exosome core component gene that is responsible for a human disease and further implicate dysregulation of RNA processing in cerebellar and spinal motor neuron maldevelopment and degeneration.     

Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of α-dystroglycan

Walker-Warburg syndrome (WWS) is an autosomal recessive multisystem disorder characterized by complex eye and brain abnormalities with congenital muscular dystrophy (CMD) and aberrant a-dystroglycan glycosylation. Here we report mutations in the ISPD gene (encoding isoprenoid synthase domain containing) as the second most common cause of WWS. Bacterial IspD is a nucleotidyl transferase belonging to a large glycosyltransferase family, but the role of the orthologous protein in chordates is obscure to date, as this phylum does not have the corresponding non-mevalonate isoprenoid biosynthesis pathway. Knockdown of ispd in zebrafish recapitulates the human WWS phenotype with hydrocephalus, reduced eye size, muscle degeneration and hypoglycosylated a-dystroglycan. These results implicate ISPD in a-dystroglycan glycosylation in maintaining sarcolemma integrity in vertebrates.     

Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.     

Mutations in CTC1, encoding conserved telomere maintenance component 1, cause Coats plus

Coats plus is a highly pleiotropic disorder particularly affecting the eye, brain, bone and gastrointestinal tract. Here, we show that Coats plus results from mutations in CTC1, encoding conserved telomere maintenance component 1, a member of the mammalian homolog of the yeast heterotrimeric CST telomeric capping complex. Consistent with the observation of shortened telomeres in an Arabidopsis CTC1 mutant and the phenotypic overlap of Coats plus with the telomeric maintenance disorders comprising dyskeratosis congenita, we observed shortened telomeres in three individuals with Coats plus and an increase in spontaneous γH2AX-positive cells in cell lines derived from two affected individuals. CTC1 is also a subunit of the α-accessory factor (AAF) complex, stimulating the activity of DNA polymerase-α primase, the only enzyme known to initiate DNA replication in eukaryotic cells. Thus, CTC1 may have a function in DNA metabolism that is necessary for but not specific to telomeric integrity.     

Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome

We identified de novo truncating mutations in ARID1B in three individuals with Coffin-Siris syndrome (CSS) by exome sequencing. Array-based copy-number variation (CNV) analysis in 2,000 individuals with intellectual disability revealed deletions encompassing ARID1B in 3 subjects with phenotypes partially overlapping that of CSS. Taken together with published data, these results indicate that haploinsufficiency of the ARID1B gene, which encodes an epigenetic modifier of chromatin structure, is an important cause of CSS and is potentially a common cause of intellectual disability and speech impairment.     

Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

Streptococcus pneumoniae ('pneumococcus') causes an estimated 14.5 million cases of serious disease and 826,000 deaths annually in children under 5 years of age(1). The highly effective introduction of the PCV7 pneumococcal vaccine in 2000 in the United States(2,3) provided an unprecedented opportunity to investigate the response of an important pathogen to widespread, vaccine-induced selective pressure. Here, we use array-based sequencing of 62 isolates from a US national monitoring program to study five independent instances of vaccine escape recombination(4), showing the simultaneous transfer of multiple and often large (up to at least 44 kb) DNA fragments. We show that one such new strain quickly became established, spreading from east to west across the United States. These observations clarify the roles of recombination and selection in the population genomics of pneumococcus and provide proof of principle of the considerable value of combining genomic and epidemiological information in the surveillance and enhanced understanding of infectious diseases.     

Distribution of Brechmorhoga clubskimmers (Odonata: Libellulidae) in the Grand Canyon region, southwestern USA

We examined the distribution of Brechmorhoga mendax and B. pertinax (Libellulidae) in northern Arizona and southern Nevada. Brechmorhoga mendax occurs widely throughout the Southwest and in Arizona up to the Mogollon Rim, and up the Colorado River from the west to at least River Mile 132 (downstream from Lees Ferry, Arizona) at elevations of 110-1460 m. In Grand Canyon it occurs along small to large tributaries and on the mainstream at elevations below 650 m. The only previously reported locality for B. pertinax in the United States is in southeastern Arizona, where it was presumed to be accidental. We report B. pertinax along 5 small, perennial tributaries emanating from Redwall Formation aquifer springs on the south side of central Grand Canyon. Those springs habitats may be threatened by regional groundwater depletion. Brechmorhoga pertinax appears to be somewhat more stenotolerant in its habitat requirements than B. mendax , a finding in keeping with these differences in range. The presence of isolated populations of B. pertinax in Grand Canyon is an example of a Neotropical influence on the fauna and indicates biogeographic corridor and refuge functions of this large, deep canyon.     

Effects of land clearing on bordering winter annual populations in the Mohave Desert

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Construction of a 10-MWe solar thermal power plant in Daggett, California, involved clearing and leveling 53 ha of desert land. Transient offsite effects of this construction were apparent as a reduced density of annual plants within 100 m downwind of the edge of the cleared area. Schismus arabicus populations recovered within four years, but Erodium cicutarium populations did not. The effects appeared to be related more to an interaction of seed-dispersal mechanisms with the large, open space than to the obvious sand movement and deposition associated with the clearing operations.     

List of Idaho Scolytidae (Coleoptera) and notes on new records

Reported are 105 species of Scolytidae (Coleoptera) from Idaho. About one-third of these are rarely collected, of which 22 species are known from a single locality each. Twelve species reported from Idaho for the first time are: Carphoborus carri Swaine, C. sansoni Swaine, Phloeosinus hoferi Blackman, Conophthorus monophyllae Hopkins, Dryocoetes betulae Hopkins, Ips confuses (LeConte), Pityophthorus absonus Blackman, P. aquilus Blackman , P. blandus Blackman, P. deletus LeConte, P. sculptor Blackman, and Xyleborinus saxeseni (Ratzeburg). Significant extensions of the known distributions in Idaho are reported for seven other scolytids; Alniphagus aspericollis (LeConte), Dendroctonus murrayanae Hopkins, Phloeotribus lecontei Schedl, Procryphalus mucronatus (LeConte), Trypophloeus populi Hopkins, Xyleborus dispar (Fabricius), and X. intrusus Blandford. Xyleborus dispar especially needs study in anticipation that it may become increasingly important in Idaho fruit trees and other woody plants including ornamentals and shade trees.