Pitfalls in single clone crispr-cas9 mutagenesis to fine-map regulatory intervals

The majority of genetic variants affecting complex traits map to regulatory regions of genes, and typically lie in credible intervals of 100 or more SNPs. Fine mapping of the causal variant(s) at a locus depends on assays that are able to discriminate the effects of polymorphisms or mutations on gene expression. Here, we evaluated a moderate-throughput CRISPR-Cas9 mutagenesis approach, based on replicated measurement of transcript abundance in single-cell clones, by deleting candidate regulatory SNPs, affecting four genes known to be affected by large-effect expression Quantitative Trait Loci (eQTL) in leukocytes, and using Fluidigm qRT-PCR to monitor gene expression in HL60 pro-myeloid human cells. We concluded that there were multiple constraints that rendered the approach generally infeasible for fine mapping. These included the non-targetability of many regulatory SNPs, clonal variability of single-cell derivatives, and expense. Power calculations based on the measured variance attributable to major sources of experimental error indicated that typical eQTL explaining 10% of the variation in expression of a gene would usually require at least eight biological replicates of each clone. Scanning across credible intervals with this approach is not recommended

Synaptic Wnt signaling—a contributor to major psychiatric disorders?

Wnt signaling is a key pathway that helps organize development of the nervous system. It influences cell proliferation, cell fate, and cell migration in the developing nervous system, as well as axon guidance, dendrite development, and synapse formation. Given this wide range of roles, dysregulation of Wnt signaling could have any number of deleterious effects on neural development and thereby contribute in many different ways to the pathogenesis of neurodevelopmental disorders. Some major psychiatric disorders, including schizophrenia, bipolar disorder, and autism spectrum disorders, are coming to be understood as subtle dysregulations of nervous system development, particularly of synapse formation and maintenance. This review will therefore touch on the importance of Wnt signaling to neurodevelopment generally, while focusing on accumulating evidence for a synaptic role of Wnt signaling. These observations will be discussed in the context of current understanding of the neurodevelopmental bases of major psychiatric diseases, spotlighting schizophrenia, bipolar disorder, and autism spectrum disorder. In short, this review will focus on the potential role of synapse formation and maintenance in major psychiatric disorders and summarize evidence that defective Wnt signaling could contribute to their pathogenesis via effects on these late neural differentiation processes

State of the Antarctic and Southern Ocean Climate System

This paper reviews developments in our understanding of the state of the Antarctic and Southern Ocean climate and its relation to the global climate system over the last few millennia. Climate over this and earlier periods has not been stable, as evidenced by the occurrence of abrupt changes in atmospheric circulation and temperature recorded in Antarctic ice core proxies for past climate. Two of the most prominent abrupt climate change events are characterized by intensification of the circumpolar westerlies (also known as the Southern Annular Mode) between ∼6000 and 5000 years ago and since 1200–1000 years ago. Following the last of these is a period of major trans-Antarctic reorganization of atmospheric circulation and temperature between A.D. 1700 and 1850. The two earlier Antarctic abrupt climate change events appear linked to but predate by several centuries even more abrupt climate change in the North Atlantic, and the end of the more recent event is coincident with reorganization of atmospheric circulation in the North Pacific. Improved understanding of such events and of the associations between abrupt climate change events recorded in both hemispheres is critical to predicting the impact and timing of future abrupt climate change events potentially forced by anthropogenic changes in greenhouse gases and aerosols. Special attention is given to the climate of the past 200 years, which was recorded by a network of recently available shallow firn cores, and to that of the past 50 years, which was monitored by the continuous instrumental record. Significant regional climate changes have taken place in the Antarctic during the past 50 years. Atmospheric temperatures have increased markedly over the Antarctic Peninsula, linked to nearby ocean warming and intensification of the circumpolar westerlies. Glaciers are retreating on the peninsula, in Patagonia, on the sub-Antarctic islands, and in West Antarctica adjacent to the peninsula. The penetration of marine air masses has become more pronounced over parts of West Antarctica. Above the surface, the Antarctic troposphere has warmed during winter while the stratosphere has cooled year-round. The upper kilometer of the circumpolar Southern Ocean has warmed, Antarctic Bottom Water across a wide sector off East Antarctica has freshened, and the densest bottom water in the Weddell Sea has warmed. In contrast to these regional climate changes, over most of Antarctica, near-surface temperature and snowfall have not increased significantly during at least the past 50 years, and proxy data suggest that the atmospheric circulation over the interior has remained in a similar state for at least the past 200 years. Furthermore, the total sea ice cover around Antarctica has exhibited no significant overall change since reliable satellite monitoring began in the late 1970s, despite large but compensating regional changes. The inhomogeneity of Antarctic climate in space and time implies that recent Antarctic climate changes are due on the one hand to a combination of strong multidecadal variability and anthropogenic effects and, as demonstrated by the paleoclimate record, on the other hand to multidecadal to millennial scale and longer natural variability forced through changes in orbital insolation, greenhouse gases, solar variability, ice dynamics, and aerosols. Model projections suggest that over the 21st century the Antarctic interior will warm by 3.4° ± 1°C, and sea ice extent will decrease by ∼30%. Ice sheet models are not yet adequate enough to answer pressing questions about the effect of projected warming on mass balance and sea level. Considering the potentially major impacts of a warming climate on Antarctica, vigorous efforts are needed to better understand all aspects of the highly coupled Antarctic climate system as well as its influence on the Earth\u27s climate and oceans

Southern Hemisphere atmospheric history of carbon monoxide over the late Holocene reconstructed from multiple Antarctic ice archives

Abstract. Carbon monoxide (CO) is a naturally occurring atmospheric trace gas, a regulated pollutant, and one of the main components determining the oxidative capacity of the atmosphere. Evaluating climate–chemistry models under different conditions than today and constraining past CO sources requires a reliable record of atmospheric CO mixing ratios ([CO]) that includes data since preindustrial times. Here, we report the first continuous record of atmospheric [CO] for Southern Hemisphere (SH) high latitudes over the past 3 millennia. Our continuous record is a composite of three high-resolution Antarctic ice core gas records and firn air measurements from seven Antarctic locations. The ice core gas [CO] records were measured by continuous flow analysis (CFA), using an optical feedback cavity-enhanced absorption spectrometer (OF-CEAS), achieving excellent external precision (2.8–8.8 ppb; 2σ) and consistently low blanks (ranging from 4.1±1.2 to 7.4±1.4 ppb), thus enabling paleo-atmospheric interpretations. Six new firn air [CO] Antarctic datasets collected between 1993 and 2016 CE at the DE08-2, DSSW19K, DSSW20K, South Pole, Aurora Basin North (ABN), and Lock-In sites (and one previously published firn CO dataset at Berkner) were used to reconstruct the atmospheric history of CO from ∼1897 CE, using inverse modeling that incorporates the influence of gas transport in firn. Excellent consistency was observed between the youngest ice core gas [CO] and the [CO] from the base of the firn and between the recent firn [CO] and atmospheric [CO] measurements at Mawson station (eastern Antarctica), yielding a consistent and contiguous record of CO across these different archives. Our Antarctic [CO] record is relatively stable from −835 to 1500 CE, with mixing ratios within a 30–45 ppb range (2σ). There is a ∼5 ppb decrease in [CO] to a minimum at around 1700 CE during the Little Ice Age. CO mixing ratios then increase over time to reach a maximum of ∼54 ppb by ∼1985 CE. Most of the industrial period [CO] growth occurred between about 1940 to 1985 CE, after which there was an overall [CO] decrease, as observed in Greenland firn air and later at atmospheric monitoring sites and attributed partly to reduced CO emissions from combustion sources. Our Antarctic ice core gas CO observations differ from previously published records in two key aspects. First, our mixing ratios are significantly lower than reported previously, suggesting that previous studies underestimated blank contributions. Second, our new CO record does not show a maximum in the late 1800s. The absence of a [CO] peak around the turn of the century argues against there being a peak in Southern Hemisphere biomass burning at this time, which is in agreement with (i) other paleofire proxies such as ethane or acetylene and (ii) conclusions reached by paleofire modeling. The combined ice core and firn air [CO] history, spanning −835 to 1992 CE, extended to the present by the Mawson atmospheric record, provides a useful benchmark for future atmospheric chemistry modeling studies

Southern Ocean carbon sink enhanced by sea-ice feedbacks at the Antarctic Cold Reversal

The Southern Ocean occupies 14% of the Earth’s surface and plays a fundamental role in the global carbon cycle and climate. It provides a direct connection to the deep ocean carbon reservoir through biogeochemical processes that include surface primary productivity, remineralization at depth and the upwelling of carbon-rich water masses. However, the role of these different processes in modulating past and future air–sea carbon flux remains poorly understood. A key period in this regard is the Antarctic Cold Reversal (ACR, 14.6–12.7 kyr bp), when mid- to high-latitude Southern Hemisphere cooling coincided with a sustained plateau in the global deglacial increase in atmospheric CO2. Here we reconstruct high-latitude Southern Ocean surface productivity from marine-derived aerosols captured in a highly resolved horizontal ice core. Our multiproxy reconstruction reveals a sustained signal of enhanced marine productivity across the ACR. Transient climate modelling indicates this period coincided with maximum seasonal variability in sea-ice extent, implying that sea-ice biological feedbacks enhanced CO2 sequestration and created a substantial regional marine carbon sink, which contributed to the plateau in CO2 during the ACR. Our results highlight the role Antarctic sea ice plays in controlling global CO2, and demonstrate the need to incorporate such feedbacks into climate–carbon models