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We use a suite of decadal-length regional climate simulations to quantify potential changes in population-weighted heat and cold exposure in 47 US metropolitan regions during the 21st century. Our results show that population-weighted exposure to locally defined extreme heat (i.e., “population heat exposure”) would increase by a factor of 12.7–29.5 under a high-intensity greenhouse gas (GHG) emissions and urban development pathway. Additionally, end-of-century population cold exposure is projected to rise by a factor of 1.3–2.2, relative to start-of-century population cold exposure. We identify specific metropolitan regions in which population heat exposure would increase most markedly and characterize the relative significance of various drivers responsible for this increase. The largest absolute changes in population heat exposure during the 21st century are projected to occur in major US metropolitan regions like New York City (NY), Los Angeles (CA), Atlanta (GA), and Washington DC. The largest relative changes in population heat exposure (i.e., changes relative to start-of-century) are projected to occur in rapidly growing cities across the US Sunbelt, for example Orlando (FL), Austin (TX), Miami (FL), and Atlanta. The surge in population heat exposure across the Sunbelt is driven by concurrent GHG-induced warming and population growth which, in tandem, could strongly compound population heat exposure. Our simulations provide initial guidance to inform the prioritization of urban climate adaptation measures and policy.

Author(s): Stoneburg, Brittney E.; McDonald, Andrew T.; Dooley, Jr., Alton C.; Scott, Eric; Hohman, Charlotte J.H. | Abstract: New material of three equids is described from the middle Miocene Cajon Valley Formation in San Bernardino National Forest, San Bernardino County, California. The material includes teeth of Archaeohippus mourningi, Scaphohippus sumani, and Parahippus brevidens. Scaphohippus intermontanus is considered a junior subjective synonym of S. sumani. Parahippus brevidens is identified from an upper molar that closely resembles the morphology of the holotype as well as referred specimens of Pa. brevidens from the Mascall Formation in Oregon and the Temblor Formation in California. The presence of Pa. brevidens in the Cajon Valley Formation represents a geographic range extension for the taxon of over 400 km. Interesting ecological implications emerge for the Cajon Valley Formation when compared to the nearby Barstow Formation, including the presence of chalicotheres and apparent lack of Hypohippus affinis and Megahippus mckennai.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0–0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875–625 and ~200–50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus. © 2021 John Wiley & Sons Ltd 19-05-00477, AAAA-A19-119032590102-7; National Science Foundation, NSF: ARC-1417036; Gordon and Betty Moore Foundation, GBMF: 3804; University of California, Santa Cruz, UCSC; U.S. Bureau of Land Management, BLM; Horizon 2020 Framework Programme, H2020: 681605; Seventh Framework Programme, FP7: IEF-302617; Natural Sciences and Engineering Research Council of Canada, NSERC; Marie Curie; European Research Council, ERC; Svenska Forskningsrådet Formas: 2018-01640; Russian Foundation for Basic Research, РФФИ: 18-04-00327; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR; Science for Life Laboratory, SciLifeLab We are grateful to the placer gold mining community, the Tr’ondëk Hwëch’in First Nation, and the Vuntut Gwitchin First Nation for their collaboration and support with our research in Yukon. Tamara Pico, Sarah Crump and Paul Koch provided advice interpreting the palaeoclimate of Beringia. Data generation was supported with funds from NSF ARC-1417036, the Gordon & Betty Moore Foundation (no. 3804) and the American Wild Horse Campaign. A.O.V. was additionally supported by a UCSC Chancellor’s Dissertation Year Fellowship and the CANA Foundation. M.T. and D.G. were supported by the Russian Foundation for Basic Research (project 18-04-00327), and L.E. by a Marie-Curie Intra-European fellowship (FP7, IEF-302617). G.B. is supported by the Federal theme of Zoological Institute of the Russian Academy of Sciences no. AAAA-A19-119032590102-7. S.V. was funded by the Russian Foundation for Basic Research, Grant 19-05-00477. L.D. acknowledges support from FORMAS (project 2018-01640). D.F. was supported by the Natural Science and Engineering Research Council. P.G. and D.M. are supported by the Bureau of Land Management. We acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. L.O. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 681605). We are grateful to the placer gold mining community, the Tr?ond?k Hw?ch?in First Nation, and the Vuntut Gwitchin First Nation for their collaboration and support with our research in Yukon. Tamara Pico, Sarah Crump and Paul Koch provided advice interpreting the palaeoclimate of Beringia. Data generation was supported with funds from NSF ARC-1417036, the Gordon & Betty Moore Foundation (no. 3804) and the American Wild Horse Campaign. A.O.V. was additionally supported by a UCSC Chancellor?s Dissertation Year Fellowship and the CANA Foundation. M.T. and D.G. were supported by the Russian Foundation for Basic Research (project 18-04-00327), and L.E. by a Marie-Curie Intra-European fellowship (FP7, IEF-302617). G.B. is supported by the Federal theme of Zoological Institute of the Russian Academy of Sciences no. AAAA-A19-119032590102-7. S.V. was funded by the Russian Foundation for Basic Research, Grant 19-05-00477. L.D. acknowledges support from FORMAS (project 2018-01640). D.F. was supported by the Natural Science and Engineering Research Council. P.G. and D.M. are supported by the Bureau of Land Management. We acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. L.O. received funding from the European Research Council (ERC) under the European Union?s Horizon 2020 research and innovation programme (grant agreement 681605).

The CD44 receptor is common among many cancer types where overexpression is synonymous with poor prognosis in prostate, glioma, and breast cancer. More notably CD44 overexpression has been shown in a number of different cancer stem cells (CSC) which are present in many solid tumors and drive growth, recurrence, and resistance to conventional therapies. Triple negative breast cancer CSCs correlate to worse prognosis and early relapse due to higher drug resistance and increased tumor heterogeneity and thus are prime targets for anticancer therapy. To specifically target cells overexpressing CD44 receptors, including CSCs, we synthesized a pentameric nanocomplex (PNC) containing gold nanoparticles, doxorubicin (Dox) conjugated to thiolated hyaluronic acid via an acid-labile hydrazone bond, and thiolated poly(ethylene glycol) DNA CD44 aptamer. In vitro drug release was highest at 8 h time point at acidic pH (pH 4.7) and in 10 mM glutathione. The PNC is almost an order of magnitude more effective than Dox alone in CD44+ cells versus CD44 low cells. Functionally, the PNC reduced CSC self-renewal. The PNC provides a therapeutic strategy that can improve the efficiency of Dox and decrease nontargeted toxicity thereby prolonging its use to individual patients.

TPS3142 Background: Protein tyrosine kinase 7 (PTK7) is a highly conserved receptor tyrosine kinase involved in the Wnt signaling pathway and is overexpressed in multiple cancer types, including non-small cell lung cancer (NSCLC). Cofetuzumab pelidotin (ABBV-647) is an anti-PTK7 antibody-drug conjugate comprising the hu6MO24 monoclonal antibody, a cleavable cysteine-reactive linker, and Aur0101 (an auristatin microtubule inhibitor). It has shown promising preclinical anti-tumor effects (Damelin et al. Sci Transl Med 2017;9[372]:eaag2611) and clinical activity with a manageable safety profile in a Phase 1 study in patients with advanced solid tumors, with promising anti-tumor activity noted in NSCLC (Sachdev et al. DOI: 10.1200/JCO.2018.36.15_suppl.5565). Methods: This open-label, single-arm, multicenter Phase 1b study (NCT04189614) will assess the anti-tumor activity and safety of cofetuzumab pelidotin in approximately 40 patients with PTK7-expressing, recurrent NSCLC. The primary objective is to assess the objective response rate of cofetuzumab pelidotin according to Response Evaluation Criteria in Solid Tumors version 1.1. Secondary objectives include the duration of response, progression-free survival, overall survival, and safety and tolerability. Pharmacokinetic and biomarker samples will also be collected throughout for analysis. Patients must be aged ≥18 years with an Eastern Cooperative Oncology Group performance status of 0–1 and have recurrent histologically confirmed NSCLC with PTK7-expressing tumor (using a validated immunohistochemistry assay). Patients must have progressed after treatment with a platinum-based chemotherapy doublet and an immune checkpoint inhibitor (for tumors without targetable genetic alterations), or a platinum-based chemotherapy doublet and targeted agent(s) (for tumors with targetable genetic alterations). Patients must also have received ≤2 prior lines of systemic therapy (≤3 prior lines for tumors treated with targeted agent[s] for genetic alterations), including no more than 1 line of systemic chemotherapy. Cofetuzumab pelidotin (2.8 mg/kg) is administered intravenously every 3 weeks until the patient experiences disease progression, intolerable toxicity, or other study treatment discontinuation criteria are met. The study commenced on February 13, 2020 and enrollment is ongoing. Clinical trial information: NCT04189614.

A middle to late Pleistocene sedimentary sequence in the upper Las Vegas Wash, north of Las Vegas, Nevada, has yielded the largest open-site Rancholabrean vertebrate fossil assemblage in the southern Great Basin and Mojave Deserts. Recent paleontologic field studies have led to the discovery of hundreds of fossil localities and specimens, greatly extending the geographic and temporal footprint of original investigations in the early 1960s. The significance of the deposits and their entombed fossils led to the preservation of 22,650 acres of the upper Las Vegas Wash as Tule Springs Fossil Beds National Monument. These discoveries also warrant designation of the assemblage as a local fauna, named for the site of the original paleontologic studies at Tule Springs. The large mammal component of the Tule Springs local fauna is dominated by remains of Mammuthus columbi as well as Camelops hesternus , along with less common remains of Equus (including E. scotti ) and Bison . Large carnivorans including Canis dirus , Smilodon fatalis , and Panthera atrox are also recorded. Micromammals, amphibians, lizards, snakes, birds, invertebrates, plant macrofossils, and pollen also occur in the deposits and provide important and complementary paleoenvironmental information. The fauna occurs within the Las Vegas Formation, an extensive and stratigraphically complex sequence of groundwater discharge deposits that represent a mosaic of desert wetland environments. Radiometric and luminescence dating indicates the sequence spans the last ∼570 ka, and records hydrologic changes in a dynamic and temporally congruent response to northern hemispheric abrupt climatic oscillations. The vertebrate fauna occurs in multiple stratigraphic horizons in this sequence, with ages of the fossils spanning from ∼100 to ∼12.5 ka.

The genus Equus originated in the Pliocene Epoch of North America, and its arrival in South America is likely related to the Great American Biotic Interchange that took place in the transition of Pliocene to Pleistocene. Currently, there are five recognized species for the South American continent: Equus neogeus, E. santaeelenae, E. insulatus, E. andium, and E. lasallei. The taxonomy of the genus is traditionally based in part upon the proportions of the autopodia. The aim of this study is to evaluate the diagnostic importance of the autopodia of South American Equus through comparative and multiple statistical analyses. Therefore, we analyzed metacarpals, metatarsals, and phalanges from all available South American Equus, with the exception of E. lasallei, which is only known by a skull. We also examined the North American species E. occidentalis, as it has been interpreted to be closely related to South American Equus. Results showed no significant differences between the various South American species according to the dimensions and proportions of the autopodia. A continuum of gradual linear variation among the species was revealed, with superimposition between autopodial characters. The succession and overlap of species indicated that the South American Equus might represent a type of cline.

Tule Springs Fossil Beds National Monument (TUSK) preserves 22,650 acres of the upper Las Vegas Wash in the northern Las Vegas Valley (Nevada, USA). TUSK is home to extensive and stratigraphically complex groundwater discharge (GWD) deposits, called the Las Vegas Formation, which represent springs and desert wetlands that covered much of the valley during the late Quaternary. The GWD deposits record hydrologic changes that occurred here in a dynamic and temporally congruent response to abrupt climatic oscillations over the last ~300 ka (thousands of years). The deposits also entomb the Tule Springs Local Fauna (TSLF), one of the most significant late Pleistocene (Rancholabrean) vertebrate assemblages in the American Southwest. The TSLF is both prolific and diverse, and includes a large mammal assemblage dominated by Mammuthus columbi and Camelops hesternus . Two (and possibly three) distinct species of Equus , two species of Bison , Panthera atrox , Smilodon fatalis , Canis dirus , Megalonyx jeffersonii , and Nothrotheriops shastensis are also present, and newly recognized faunal components include micromammals, amphibians, snakes, and birds. Invertebrates, plant macrofossils, and pollen also occur in the deposits and provide important and complementary paleoenvironmental information. This field compendium highlights the faunal assemblage in the classic stratigraphic sequences of the Las Vegas Formation within TUSK, emphasizes the significant hydrologic changes that occurred in the area during the recent geologic past, and examines the subsequent and repeated effect of rapid climate change on the local desert wetland ecosystem.

Biochronology is important to vertebrate chronology because the primary temporal units developed and applied by vertebrate paleontologists for correlation of terrestrial deposits (Land Mammal Ages, LMA) are all biochronologic units. Specific mammal biochronologic scales have been developed for Europe (MN units or ELMA), Asia (ALMA), North America (NALMA), and South America (SALMA). Each timescale is based on land mammal first appearances and characteristic associations on different continental landmasses. Herein, we summarize and review the bases for recognizing mammalian biochronologic units with the most recent update of the Land Mammal Ages. We correlate these ages with the global magnetochronostratigraphic and geochronologic time scales including the major equid evolutionary events of the last 8 million years.

A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.

The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event., eLife digest The horse family – which also includes zebras, donkeys and asses – is often featured on the pages of textbooks about evolution. All living horses belong to a group, or genus, called Equus. The fossil record shows how the ancestors of these animals evolved from dog-sized, three-toed browsers to larger, one-toed grazers. This process took around 55 million years, and many members of the horse family tree went extinct along the way. Nevertheless, the details of the horse family tree over the past 2.5 million years remain poorly understood. In North America, horses from this period – which is referred to as the Pleistocene – have been classed into two major groups: stout-legged horses and stilt-legged horses. Both groups became extinct near the end of the Pleistocene in North America, and it was not clear how they relate to one another. Based on their anatomy, many scientists suggested that stilt-legged horses were most closely related to modern-day asses living in Asia. Yet, other studies using ancient DNA placed the stilt-legged horses closer to the stout-legged horses. Heintzman et al. set out to resolve where the stilt-legged horses sit within the horse family tree by examining more ancient DNA than the previous studies. The analyses showed that the stilt-legged horses were much more distinct than previously thought. In fact, contrary to all previous findings, these animals actually belonged outside of the genus Equus. Heintzman et al. named the new genus for the stilt-legged horses Haringtonhippus, and showed that all stilt-legged horses belonged to a single species within this genus, Haringtonhippus francisci. Together these new findings provide a benchmark for reclassifying problematic fossil groups across the tree of life. A similar approach could be used to resolve the relationships in other problematic groups of Pleistocene animals, such as mammoths and bison. This would give scientists a more nuanced understanding of evolution and extinction during this period.

In 1969, Robert E. Gregg collected five species of ants (Hymenoptera: Formicidae) in three Subarctic localities near the town of Churchill, Manitoba, Canada, which he documented in a 1972 publication in The Canadian Entomologist. To determine whether there have been any additions to the local fauna – as might be predicted to occur in response to a warming climate and increased traffic to the Port of Churchill in the intervening 40 years – we re-collected ants from the same localities in 2012. We identified the ants we collected from Gregg’s sampling sites using both traditional morphological preparations and DNA barcoding. In addition, we examined specimens from Gregg’s initial collection that are accessioned at the Field Museum of Natural History (Chicago, Illinois, United States of America). Using this integrative approach we report seven species present at the same sites Gregg sampled 40 years earlier. We conclude that the apparent increase is likely not due to any arrivals from more southerly distributed ants, but to the increased resolution provided by DNA barcodes to resident species complexes with a complicated history. We provide a brief synopsis of these results and their taxonomic context.

Docosahexanoic acid (DHA) is the most abundant omega-3 fatty acid in brain, and, although it is considered essential, deficiency has not been linked to disease. Despite the large mass of DHA in phospholipids, the brain does not synthesize it. DHA is imported across the blood-brain barrier (BBB) through the major facilitator superfamily domain-containing 2a (MFSD2A) protein. MFSD2A transports DHA as well as other fatty acids in the form of lysophosphatidylcholine (LPC). We identify two families displaying MFSD2A mutations in conserved residues. Affected individuals exhibited a lethal microcephaly syndrome linked to inadequate uptake of LPC lipids. The MFSD2A mutations impaired transport activity in a cell-based assay. Moreover, when expressed in mfsd2aa-morphant zebrafish, mutants failed to rescue microcephaly, BBB breakdown and lethality. Our results establish a link between transport of DHA and LPCs by MFSD2A and human brain growth and function, presenting the first evidence of monogenic disease related to transport of DHA in humans.

Pediatric-onset ataxias often present clinically as developmental delay and intellectual disability, with prominent cerebellar atrophy as a key neuroradiographic finding. Here we describe a new clinically distinguishable recessive syndrome in 12 families with cerebellar atrophy together with ataxia, coarsened facial features and intellectual disability, due to truncating mutations in the sorting nexin gene SNX14, encoding a ubiquitously expressed modular PX domain-containing sorting factor. We found SNX14 localized to lysosomes and associated with phosphatidylinositol (3,5)-bisphosphate, a key component of late endosomes/lysosomes. Patient-derived cells showed engorged lysosomes and a slower autophagosome clearance rate upon autophagy induction by starvation. Zebrafish morphants for snx14 showed dramatic loss of cerebellar parenchyma, accumulation of autophagosomes and activation of apoptosis. Our results characterize a unique ataxia syndrome due to biallelic SNX14 mutations leading to lysosome-autophagosome dysfunction.

Dendritic spines represent the major site of neuronal activity in the brain; they serve as the receiving point for neurotransmitters and undergo rapid activity-dependent morphological changes that correlate with learning and memory. Using a combination of homozygosity mapping and next-generation sequencing in two consanguineous families affected by nonsyndromic autosomal-recessive intellectual disability, we identified truncating mutations in formin 2 (FMN2), encoding a protein that belongs to the formin family of actin cytoskeleton nucleation factors and is highly expressed in the maturing brain. We found that FMN2 localizes to punctae along dendrites and that germline inactivation of mouse Fmn2 resulted in animals with decreased spine density; such mice were previously demonstrated to have a conditioned fear-learning defect. Furthermore, patient neural cells derived from induced pluripotent stem cells showed correlated decreased synaptic density. Thus, FMN2 mutations link intellectual disability either directly or indirectly to the regulation of actin-mediated synaptic spine density.

The vertebrate record at the Ziegler Reservoir fossil site (ZRFS) near Snowmass Village, Colorado ranges from ~140 to 77 ka, spanning all of Marine Oxygen Isotope Stage (MIS) 5. The site contains at least 52 taxa of macro- and microvertebrates, including one fish, three amphibian, four reptile, ten bird, and 34 mammal taxa. The most common vertebrate isAmbystoma tigrinum(tiger salamander), which is represented by >22,000 elements representing the entire life cycle. The mastodon,Mammut americanum, is the most common mammal, and is documented by >1800 skeletal elements making the ZRFS one of the largest accumulations of proboscidean remains in North America. Faunas at the ZRFS can be divided into two groups, a lake-margin group dating to ~140–100 ka that is dominated by woodland taxa, and a lake-center group dating to ~87–77 ka characterized by taxa favoring more open conditions. The change in faunal assemblages occurred between MIS 5c and 5a (vertebrates were absent from MIS 5b deposits), which were times of significant environmental change at the ZRFS. Furthermore, the ZRFS provides a well-dated occurrence of the extinctBison latifrons, which has implications for the timing of the Rancholabrean Mammal Age in the region.

BackgroundTransport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.ObjectiveWe aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.MethodsLinkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.ResultsWe identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.ConclusionThis study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.

Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg2+-dependent 3’ end ribonucleases with mostly unknown substrate specificity1. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration with ambiguous genitalia2 (MIM%614969). We studied 12 human families with PCH7, uncovering biallelic, loss of function mutations in TOE1 (NC_000001.11), which encodes an unconventional deadenylase3,4. Toe1-morphant zebrafish displayed mid- and hind-brain degeneration, modeling PCH-like structural defects in vivo. Surprisingly, we found TOE1 associated with incompletely processed small nuclear (sn)RNAs of the spliceosome, which is responsible for pre-mRNA splicing. These pre-snRNAs contained 3’ genome-encoded tails often followed by post-transcriptionally added adenosines. Human cells with reduced levels of TOE1 accumulated 3’ end-extended pre-snRNAs, and immuno-isolated TOE1 complex was sufficient for 3’ end maturation of snRNAs. Our findings reveal the cause of a neurodegenerative syndrome linked to snRNA maturation and uncover a key factor involved in processing of snRNA 3’ ends.

PubMedID: 28013290 The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the ?/ß-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of b-tubulin to fold or become assembled into the ?/ß-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects. © The Author 2016. Published by Oxford University Press. All rights reserved.

Previous studies on transplanted tissue or single cancers indicated that cfDNA variant fragment lengths reflect their respective source. The Circulating Cell-free Genome Atlas (NCT02889978) study provides an opportunity to examine cfDNA variant fragment lengths across tumor types and describe the nature of cfDNA variants derived from different sources. Blood samples (N=1406) were evaluated from participants with (n=845) and without (n=561) cancer; cancer samples included 339 breast, 118 lung, 69 prostate, 45 colorectal, 27 uterine, 26 pancreas, 26 renal, 24 esophageal, 22 lymphoma, 19 head/neck, and 17 ovarian (113 remaining samples represented cancers with ≤15 samples each). cfDNA and genomic DNA from white blood cells (WBC) were subjected to a high-intensity targeted panel (507 genes, 60000X) with error-corrected sequencing; 533 samples also had matched tumor biopsy tissue subjected to whole-genome sequencing (30X). Somatic single-nucleotide variants (SNVs; that passed noise filters) were identified and classified using the sequencing results into one of four categories: tumor biopsy-matched (TBM; present in cfDNA and biopsy), WBC-matched (WM; present in cfDNA and WBC), non-matched (NM; low probability [P A total of 21604 SNVs were identified. The proportion of SNVs from each category were: 4% TBM, 68% WM, 19% NM, and 8% AMB. The number of samples (non-mutually exclusive) that had each SNV category were 152 TBM, 1338 WM, 499 NM, and 761 AMB. Across categories, the median (SD) length of fragments containing the reference allele was 167 (16.3). Median (SD) fragment lengths of TBM, WM, NM, and AMB were 156 (22.2), 169 (14.8), 158 (20.8), and 165 (17.8), respectively. AMB and WM median SNV fragment lengths were similar to that of the reference allele, suggesting that fragment length shifts are minimal in SNVs derived from clonal hematopoiesis (CH). Fragment lengths of TBM and NM SNVs were similar; further, most NM SNVs came from cfDNA samples in the cancer cohort, suggesting that NM SNVs may be tumor-derived. As expected in a population with a median (SD) age of 61 (12.2), most SNVs occurred in the WM category. The prediction model distinguished TBM from WM SNVs with an AUC of 0.87. However, at a specificity of 98% (to match filtering based on WBC sequencing), false-negative rates were 35% (TBM) and 52% (NM). Together, these data suggest that source prediction based on fragment length alone is less robust than source assignment using individual-matched WBC sequencing, highlighting the importance of accounting for CH-derived SNVs when using targeted cfDNA-based approaches for cancer detection. Citation Format: Earl Hubbell, Tara Maddala, Oliver Venn, Eric Scott, Susan Tang, Archana Shenoy, Alex Aravanis. Cell-free DNA (cfDNA) fragment length patterns of tumor- and blood-derived variants in participants with and without cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3372.

The corpus callosum is the principal cerebral commissure connecting the right and left hemispheres. The development of the corpus callosum is under tight genetic control, as demonstrated by abnormalities in its development in more than 1,000 genetic syndromes. We recruited more than 25 families in which members affected with corpus callosum hypoplasia (CCH) lacked syndromic features and had consanguineous parents, suggesting recessive causes. Exome sequence analysis identified C12orf57 mutations at the initiator methionine codon in four different families. C12orf57 is ubiquitously expressed and encodes a poorly annotated 126 amino acid protein of unknown function. This protein is without significant paralogs but has been tightly conserved across evolution. Our data suggest that this conserved gene is required for development of the human corpus callosum.

Objective To compare serum anti-Müllerian hormone (AMH) and other endocrine parameters between patients diagnosed with polycystic ovary syndrome (PCOS) and age-matched ovulatory women. Materials and methods AMH, DHEAS, FSH, LH, PRL, TSH and total testosterone (TT) were prospectively measured in oligo-ovulatory PCOS patients (n = 595) and in ovulatory non-PCOS women (n = 157) referred to a tertiary infertility center. Mean BMI was similar across the two study populations and there were no smokers in the sample. Patients in both groups were further classified into three categories by age: < 25 yrs, 25-34 yrs, and ≥ 35 yrs. Selected clinical and demographic characteristics were tabulated for each group. Results Serum AMH was significantly higher among PCOS patients compared to non-PCOS controls in the non-stratified sample (7.54 ± 5.8 vs. 2.49 ± 2.0 ng/mL, respectively; p < 0.0001), while serum FSH, DHEAS, TSH and prolactin were similar for both groups (p > 0.05). As expected, mean (total) testosterone levels were notably different between PCOS vs. non-PCOS controls (0.84 ± 0.76 vs. 0.43 ± 0.38 ng/mL, respectively; p < 0.001), and mean AMH level was significantly lower in the oldest age category (> 35 yrs) compared to both younger control groups (p < 0.0001). Both DHEAS and total testosterone decreased with age among PCOS patients, although mean serum DHEAS for women age > 35 yrs was significantly lower than DHEAS measured in younger women with PCOS (p < 0.02). For PCOS patients, AMH remained relatively stable irrespective of age. Conclusion Although AMH can serve as a satisfactory marker of ovarian reserve, for PCOS patients the expected decline in AMH associated with reproductive aging appears attenuated despite ovarian senescence. In contrast, mean DHEAS levels were markedly lower among older PCOS women (> 35 yrs) compared to younger PCOS patients.

The tRNA splicing endonuclease is a highly evolutionarily conserved protein complex, involved in the cleavage of intron-containing tRNAs. In human it consists of the catalytic subunits TSEN2 and TSEN34, as well as the non-catalytic TSEN54 and TSEN15. Recessive mutations in the corresponding genes of the first three are known to cause pontocerebellar hypoplasia (PCH) types 2A-C, 4, and 5. Here, we report three homozygous TSEN15 variants that cause a milder version of PCH2. The affected individuals showed progressive microcephaly, delayed developmental milestones, intellectual disability, and, in two out of four cases, epilepsy. None, however, displayed the central visual failure seen in PCH case subjects where other subunits of the TSEN are mutated, and only one was affected by the extensive motor defects that are typical in other forms of PCH2. The three amino acid substitutions impacted the protein level of TSEN15 and the stoichiometry of the interacting subunits in different ways, but all resulted in an almost complete loss of in vitro tRNA cleavage activity. Taken together, our results demonstrate that mutations in any known subunit of the TSEN complex can cause PCH and progressive microcephaly, emphasizing the importance of its function during brain development.

Biogenesis of the primary cilium, a cellular organelle mediating various signaling pathways, is generally coordinated with cell cycle exit/re-entry. Although the dynamic cell cycle-associated profile of the primary cilium has been largely accepted, the mechanism governing the link between ciliogenesis and cell cycle progression has been poorly understood. Using a human genome-wide RNAi screen, we identify genes encoding subunits of the spliceosome and proteasome as novel regulators of ciliogenesis. We demonstrate that 1) the mRNA processing-related hits are essential for RNA expression of molecules acting in cilia disassembly, such as AURKA and PLK1, and 2) the ubiquitin–proteasome systems (UPS)-involved hits are necessary for proteolysis of molecules acting in cilia assembly, such as IFT88 and CPAP. In particular, we show that these screen hit-associated mechanisms are crucial for both cilia assembly and cell cycle arrest in response to serum withdrawal. Finally, our data suggest that the mRNA processing mechanism may modulate the UPS-dependent decay of cilia assembly regulators to control ciliary resorption-coupled cell cycle re-entry.

Late Pleistocene groundwater discharge deposits (paleowetlands) in the upper Las Vegas Wash north of Las Vegas, Nevada, have yielded an abundant and diverse vertebrate fossil assemblage, the Tule Springs local fauna (TSLF). The TSLF is the largest open-site vertebrate fossil assemblage dating to the Rancholabrean North American Land Mammal Age in the southern Great Basin and Mojave Desert. Over 600 discrete body fossil localities have been recorded from the wash, including an area that now encompasses Tule Springs Fossil Beds National Monument (TUSK). Paleowetland sediments exposed in TUSK named the Las Vegas Formation span the last 250 ka, with fossiliferous sediments spanning ∼100–13 ka. The recovered fauna is dominated by remains ofCamelopsandMammuthus, and also includes relatively common remains of extinctEquusandBisonas well as abundant vertebrate microfaunal fossils. Large carnivorans are rare, with onlyPuma concolorandPanthera atroxdocumented previously. Postcranial remains assigned to the speciesCanis dirus(dire wolf) andSmilodon fatalis(sabre-toothed cat) represent the first confirmed records of these species from the TSLF, as well as the first documentation ofCanis dirusin Nevada and the only known occurrence ofSmilodonin southern Nevada. The size of the recovered canid fossil precludes assignment to other Pleistocene species ofCanis. The morphology of the felid elements differentiates them from other large predators such asPanthera,Homotherium, andXenosmilus, and the size of the fossils prevents assignment to other species ofSmilodon. The confirmed presence ofS. fatalisin the TSLF is of particular interest, indicating that this species inhabited open habitats. In turn, this suggests that the presumed preference ofS. fatalisfor closed-habitat environments hunting requires further elucidation.

Defects in clearing apoptotic debris disrupt tissue and immunological homeostasis, leading to autoimmune and inflammatory diseases. Herein, we report that macrophages from lupus-prone MRL/lpr mice have impaired lysosomal maturation, resulting in heightened ROS production and attenuated lysosomal acidification. Impaired lysosomal maturation diminishes the ability of lysosomes to degrade apoptotic debris contained within IgG-immune complexes (IgG-ICs) and promotes recycling and the accumulation of nuclear self-antigens at the membrane 72 h after internalization. Diminished degradation of IgG-ICs prolongs the intracellular residency of nucleic acids, leading to the activation of Toll-like receptors. It also promotes phagosomal membrane permeabilization, allowing dsDNA and IgG to leak into the cytosol and activate AIM2 and TRIM21. Collectively, these events promote the accumulation of nuclear antigens and activate innate sensors that drive IFN alpha production and heightened cell death. These data identify a previously unidentified defect in lysosomal maturation that provides a mechanism for the chronic activation of intracellular innate sensors in systemic lupus erythematosus.

Direct radiocarbon dating and stable isotope and biometric analyses are evidence that the holotype of Equus laurentius Hay, 1913 comprises the skull and jaw of two different horses that are less than 500 years old. The size and morphology of the specimens fall within the range of like elements of modern Equus caballus Linnaeus, 1758. The mandibular cheek teeth exhibit bit wear, demonstrating that the mandible is that of a domestic animal. The taxonomy of the purportedly late Pleistocene species is therefore resolved, and Equus laurentius Hay is a junior synonym of Equus caballus Linnaeus. Equus laurentius and its holotype are neither taxonomically nor phylogenetically pertinent to studies of North American Pleistocene Equus.

Proposed explanations for the terminal Pleistocene large mammal extinction event in North America include climate warming and/or cooling, overhunting by early humans, disease, and bolide detonation or impact. A key assumption common to all these scenarios is that large mammals present in North America near the end of the Pleistocene were also present in similar abundance, with similar geographic distributions, during earlier, equally severe periods of climate change (e.g., ∼130 ka BP). This assumption is challenged here. An important difference in the latest Pleistocene was the profusion and geographic extent of the genus Bison , particularly in the American West. During the late Pleistocene, south of the glacial ice, the species Bison antiquus was more widely distributed and present in greater profusion than earlier species such as the larger B. latifrons . The increased abundance of these large, aggressive, herd-dwelling ruminants in the late Pleistocene constitutes a critical difference between this time period and earlier, similarly intense interglacials. Extinction scenarios for Pleistocene North America should avoid assuming a relatively static long-term faunal component, and account for the impacts of non-human immigrant species on natives, particularly when immigration events are close in time and space with climate changes.

Defective primary ciliogenesis or cilium stability forms the basis of human ciliopathies, including Joubert syndrome (JS), with defective cerebellar vermis development. We performed a high-content genome-wide small interfering RNA (siRNA) screen to identify genes regulating ciliogenesis as candidates for JS. We analyzed results with a supervised-learning approach, using SYSCILIA gold standard, Cildb3.0, a centriole siRNA screen and the GTex project, identifying 591 likely candidates. Intersection of this data with whole exome results from 145 individuals with unexplained JS identified six families with predominantly compound heterozygous mutations in KIAA0586. A c.428del base deletion in 0.1% of the general population was found in trans with a second mutation in an additional set of 9 of 163 unexplained JS patients. KIAA0586 is an orthologue of chick Talpid3, required for ciliogenesis and Sonic hedgehog signaling. Our results uncover a relatively high frequency cause for JS and contribute a list of candidates for future gene discoveries in ciliopathies. DOI: http://dx.doi.org/10.7554/eLife.06602.001, eLife digest Joubert syndrome is a rare disorder that affects the brain and causes physical, mental, and sometimes visual impairments. In individuals with this condition, two parts of the brain called the cerebellar vermis and the brainstem do not develop properly. This is thought to be due to defects in the development and maintenance of tiny hair-like structures called cilia, which are found on the surface of cells. Currently, mutations in 25 different genes are known to be able to cause Joubert syndrome. However, these mutations only account for around 50% of the cases that have been studied, and the ‘unexplained’ cases suggest that mutations in other genes may also cause the disease. Here, Roosing et al. used a technique called a ‘genome-wide siRNA screen’ to identify other genes regulating the formation of cilia that might also be connected with Joubert syndrome. This approach identified almost 600 candidate genes. The data from the screen were combined with gene sequence data from 145 individuals with unexplained Joubert syndrome. Roosing et al. found that individuals with Joubert syndrome from 15 different families had mutations in a gene called KIAA0586. In chickens and mice, this gene—known as Talpid3—is required for the formation of cilia. Roosing et al.'s findings reveal a new gene that is involved in Joubert syndrome and also provides a list of candidate genes for future studies of other conditions caused by defects in the formation of cilia. The next challenges are to find out what causes the remaining unexplained cases of the disease and to understand what roles the genes identified in this study play in cilia. DOI: http://dx.doi.org/10.7554/eLife.06602.002

The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

Mid-Pleistocene vertebrates in North America are scarce but important for recognizing the ecological effects of climatic change in the absence of humans. We report on a uniquely rich mid-Pleistocene vertebrate sequence from Porcupine Cave, Colorado, which records at least 127 species and the earliest appearances of 30 mammals and birds. By analyzing >20,000 mammal fossils in relation to modern species and independent climatic proxies, we determined how mammal communities reacted to presumed glacial–interglacial transitions between 1,000,000 and 600,000 years ago. We conclude that climatic warming primarily affected mammals of lower trophic and size categories, in contrast to documented human impacts on higher trophic and size categories historically. Despite changes in species composition and minor changes in small-mammal species richness evident at times of climatic change, overall structural stability of mammal communities persisted >600,000 years before human impacts.

Next-generation sequencing (NGS) has made it possible to identify about 20,000 variants in the protein-coding exome of each individual, of which only a few are likely to underlie a genetic disease. Variant-level methods such as PolyPhen-2, SIFT and CADD are useful for obtaining a prediction as to whether a given variant is benign/damaging1–3 or tolerant/intolerant1–3 (we hereafter use the terms benign/deleterious). These methods are commonly interpreted in a binary manner for filtering out benign variants from NGS data, with a single significance cutoff value across all protein-coding genes. PolyPhen-2 and SIFT integrate the fixed cutoff in the software. CADD proposed (but did not recommend for categorical usage) the fixed value of 15 (or another value between 10 and 20). Gene-level methods, such as RVIS, de novo excess and GDI are also useful4–6. Combining fixed gene-level and variant-level cutoffs is also applied in the RVIS hot zone approach4. However, owing to the diversity of medical and population genetic features between human genes and across populations, a uniform cutoff is unlikely to be accurate genome-wide.

To compare standard density gradient centrifugation sperm preparation with a novel non-centrifugation-based dual-chamber capillary dish in efficiency for motile human sperm separation, approximately 3 mL fresh ejaculate specimens was obtained from 21 men (median age = 32 years. range 26-42 years) undergoing infertility evaluation. For each specimen, half of the sample was processed with a standard 45%/90% density gradient preparation (PureSperm. Nidacon International, Gothenburg, Sweden) followed by semen analysis. The other half was incubated in the Zech glass capillary dish (Astromedtec, Salzburg, Austria) consisting of 2 concentric wells overlaid by a U-ring and coverglass. After approximately 3 h, a 1-mL sample was taken from the central chamber and analyzed. Percentage motile sperm recovery, absolute (motile) cell number, and path velocities were compared for spermatozoa obtained from both methods. Both techniques reduced overall sperm concentration while enriching specimens with more motile spermatozoa. A trend towards higher % recovery of motile spermatozoa (p = .264) was observed with the Zech device, but at a cost of fewer absolute numbers of higher velocity cells (p = .004). The Zech device, therefore, localized a very small population of motile sperm without exposure to centrifugation stress, which has been considered potentially harmful to spermatozoa. This technique could theoretically improve efficiency by reducing time required to identify motile cells in in vitro fertilization where intracytoplasmic sperm injection is planned. However, refinements in incubation interval and suspension volumes are needed before this technique can be considered comparable to the density gradient method in recovering sperm for use in intrauterine insemination.

Neurodegenerative Genetics The underlying genetics of neurodegenerative disorders tend not to be well understood. Novarino et al. (p. 506 ; see the Perspective by Singleton ) investigated the underlying genetics of hereditary spastic paraplegia (HSP), a human neurodegenerative disease, by sequencing the exomes of individuals with recessive neurological disorders. Loss-of-function gene mutations in both novel genes and genes previously implicated for this condition were identified, and several were functionally validated.

Contains fulltext : 137504.pdf (Publisher’s version ) (Open Access) Joubert syndrome and related disorders (JSRDs) are genetically heterogeneous and characterized by a distinctive mid-hindbrain malformation. Causative mutations lead to primary cilia dysfunction, which often results in variable involvement of other organs such as the liver, retina, and kidney. We identified predicted null mutations in CSPP1 in six individuals affected by classical JSRDs. CSPP1 encodes a protein localized to centrosomes and spindle poles, as well as to the primary cilium. Despite the known interaction between CSPP1 and nephronophthisis-associated proteins, none of the affected individuals in our cohort presented with kidney disease, and further, screening of a large cohort of individuals with nephronophthisis demonstrated no mutations. CSPP1 is broadly expressed in neural tissue, and its encoded protein localizes to the primary cilium in an in vitro model of human neurogenesis. Here, we show abrogated protein levels and ciliogenesis in affected fibroblasts. Our data thus suggest that CSPP1 is involved in neural-specific functions of primary cilia.

Honoring a renowned specialist in studies of ancient horses, Equids in Time and Space: Papers in Honour of Vera Eisenmann edited by Marjan Mashkour includes 18 chapters by 22 international paleontologists, archaeologists, anatomists, historians, and other experts on living and extinct Equus and related horse relatives. There is also an introduction providing a brief review of Dr. Eisenmann’s life and career. The volume is not without some substantial flaws, but remains a useful acquisition for anyone interested in the history and prehistory of these important animals. The book is hardcover and oversize. Typeface is generally clean and sharp; figures are grayscale and of varying quality, depending upon the author(s). The volume is divided into five more or less equally-weighted sections: geographic distribution, Paleolithic horses, domestication, methodology, and anthropozoology. Equids earlier than the latest Tertiary and Quaternary are not discussed in any detail, reflecting Dr. Eisenmann’s focus on more geologically recent horses. The investigative approaches employed are extremely diverse, including historic and paleontologic literature reviews, interpretations of old and new metric indices, uniand multivariate statistical analyses, and assessments of stable isotope chemistry in fossil equid teeth. The four papers comprising the geographic distribution portion of the volume demonstrate the diversity of investigative methods employed. Deng reviews late Pleistocene Przewalski’s horses from China, using carbon isotopes from dental enamel to suggest that Przewalski’s horses, as arid-adapted animals, can be used to track the waxing and waning of the East Asian monsoon through time. Foronova examines numerous late Pleistocene sites in southern Siberia, determining through dental morphology and morphometric analyses of metapodials that caballine and hemionine horses were all present in the region, but in varying abundance through time depending upon local climate. Pichardo reviews the published literature on late Pleistocene horses from North and South America; this study is unfortunately hampered by an unfocused presentation and an incomplete selection of reference works [several important J Mammal Evol (2008) 15:147–149 DOI 10.1007/s10914-007-9063-5

Previous results from remains of tusks, teeth and bones collected from Wrangel Island (Vartanyan et al. 1995) had given results in the range 3730 bp to 20,000 bp and the authors had concluded that “mammoths inhabited Wrangel Island for as long as 6000 yr after the estimated extinction on the Siberian continent”. There still remained the question of the earliest date for such remains. Further, the authors had noted such samples may present some difficulty in dating and therefore duplicate samples had been measured in a second laboratory with satisfactory results. The replicate dating of important or controversial samples in more than one laboratory is well-established (e.g., Turin Shroud) and in this paper, we present results for 5 mammoth samples dated by 6 laboratories. Such interlaboratory comparisons provide an independent means of verification of laboratory comparability, and give added confidence in the results, particularly when applied to more controversial samples. A further objective of the work has been to evaluate the material for inclusion in any large-scale interlaboratory comparison, such comparisons having in the past formed part of laboratory quality assurance protocols. The design and organization of a laboratory intercomparison requires homogeneous samples in sufficient quantity to satisfy participants, and so in principle, a single mammoth tusk would meet these criteria. Samples such as the mammoth tusk have been used in previous intercomparisons: e.g., in the last large-scale international intercomparison (Gulliksen and Scott 1995), whalebone was one of the materials distributed. One of the key advantages of such material is that a single sample (a mammoth tusk) can be resampled for analysis by multiple labs and thus does not require bulk homogenization. Therefore, as part of a preselection process for a future intercomparison, five samples from separate mammoth tusks were collected from Wrangel Island in 1995 in sufficient quantity to allow multiple dating. The aim was to identify five separate samples of young age, sample up to 1 kg from each tusk and mark the location so that after preliminary dating, samples could be retrieved as required in the future. Six laboratories received samples for dating. The paper will discuss the results from the laboratories, present consensus values, and make recommendations concerning use of these samples in a future laboratory intercomparison.

Interlaboratory comparisons have been widely used in analytical chemistry and radiochemistry as an important part of ongoing quality assurance programs. The 14C community has been no exception in this respect, and in just under 20 years, there have been a number of significant and very extensive interlaboratory trials organized by individual laboratories and the International Atomic Energy Agency (IAEA) to the benefit of the 14C community (both labs and users) (Otlet et al. 1980; ISG 1982; Scott et al. 1990; Rozanski et al. 1992; Scott et al. 1992; Gulliksen and Scott 1995). The comparisons have varied widely in terms of sample type and preparation, but all have had as their primary goal the investigation of the comparability of results produced under possibly quite different laboratory protocols. As techniques have been developed and new labs formed, the reference materials created as a result of the intercomparisons have presented an opportunity for checking procedures and results. Users have been reassured by the existence of regular comparisons as one sign of the concern that laboratories have to ensure highest quality results, but also confused about how to make use of the results from past exercises in the interpretation of sets of dates from many laboratories. The laboratories have also learned valuable lessons from participation in such studies. These have included identification of systematic offsets and additional sources of variation and in studies which have used realistic samples requiring pretreatment, chemical synthesis and counting, it has been possible to identify the stage at which such problems have arisen and to quantify the relative contributions to the overall variation. In this paper, we will briefly review the comparisons so far, draw some conclusions from their findings, and make proposals for the future organization of intercomparisons.

Fossil sales are big business. Major auction houses such as Sotheby's and Bonhams & Butterfields proudly feature fossils, including vertebrate fossils, in their catalogues. On online auction sites such as eBay, fossil dealers offer museum-quality specimens for private ownership at prices ranging from around a dollar to several thousands of dollars. For example, searches conducted on eBay during the writing of this manuscript, using the key words “dinosaur fossil,” gave results consistently showing around 200 items; items priced in U.S. dollars fetched a cumulative price tag consistently in excess of $21,000. Clearly, there's money to be made in selling vertebrate fossils for profit. Given this, it might come as a surprise to the general public that many people consider fossils to be resources worth protecting, rather than commodities to be sold. For example, a bill unanimously passed by the U.S. Senate in July 2005, and currently under consideration by the U.S. House of Representatives (before the Committees of Resources and Agriculture as of this writing), the “Paleontological Resources Preservation Act” (S.263), considers fossils to be nonrenewable and scientifically important resources requiring protection and conservation. A report published in May of 2000 by then-Secretary of the Interior Bruce Babbitt recognized fossils as part of our natural heritage, further emphasizing that vertebrate fossils are rare, and that significant fossils found on public lands should be conserved for scientific and educational purposes. The Society of Vertebrate Paleontology (SVP), a professional international organization of vertebrate paleontologists, asks its members to adhere to an ethics statement specifically rejecting the idea of significant vertebrate fossils as items that can be bought, sold or bartered, save where such activities bring those fossils into the public trust. Why is there such a difference of opinion? Is it better to sell vertebrate fossils, or to preserve them in perpetuity? …

Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/.

Purine biosynthesis and metabolism, conserved in all living organisms, is essential for cellular energy homeostasis and nucleic acids synthesis. The de novo synthesis of purine precursors is under tight negative feedback regulation mediated by adenosine and guanine nucleotides. We describe a new distinct early-onset neurodegenerative condition resulting from mutations in the adenosine monophosphate deaminase 2 gene (AMPD2). Patients have characteristic brain imaging features of pontocerebellar hypoplasia (PCH), due to loss of brainstem and cerebellar parenchyma. We found that AMPD2 plays an evolutionary conserved role in the maintenance of cellular guanine nucleotide pools by regulating the feedback inhibition of adenosine derivatives on de novo purine synthesis. AMPD2 deficiency results in defective GTP-dependent initiation of protein translation, which can be rescued by administration of purine precursors. These data suggest AMPD2-related PCH as a new, potentially treatable early-onset neurodegenerative disease.

Joubert syndrome and related disorders (JSRD) are clinically and genetically heterogeneous ciliopathies sharing a peculiar midbrain–hindbrain malformation known as the ‘molar tooth sign’. To date, 19 causative genes have been identified, all coding for proteins of the primary cilium. There is clinical and genetic overlap with other ciliopathies, in particular with Meckel syndrome (MKS), that is allelic to JSRD at nine distinct loci. We previously identified the INPP5E gene as causative of JSRD in seven families linked to the JBTS1 locus, yet the phenotypic spectrum and prevalence of INPP5E mutations in JSRD and MKS remain largely unknown. To address this issue, we performed INPP5E mutation analysis in 483 probands, including 408 JSRD patients representative of all clinical subgroups and 75 MKS fetuses. We identified 12 different mutations in 17 probands from 11 JSRD families, with an overall 2.7% mutation frequency among JSRD. The most common clinical presentation among mutated families (7/11, 64%) was Joubert syndrome with ocular involvement (either progressive retinopathy and/or colobomas), while the remaining cases had pure JS. Kidney, liver and skeletal involvement were not observed. None of the MKS foetuses carried INPP5E mutations, indicating that the two ciliopathies are not allelic at this locus., peer-reviewed