Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells

Background

The mitotic spindle is a complex mechanical apparatus required for accurate segregation of sister chromosomes during mitosis. We designed a genetic screen using automated microscopy to discover factors essential for mitotic progression. Using a RNA interference library of 49,164 double-stranded RNAs targeting 23,835 human genes, we performed a loss of function screen to look for small interfering RNAs that arrest cells in metaphase.

Results

Here we report the identification of genes that, when suppressed, result in structural defects in the mitotic spindle leading to bent, twisted, monopolar, or multipolar spindles, and cause cell cycle arrest. We further describe a novel analysis methodology for large-scale RNA interference datasets that relies on supervised clustering of these genes based on Gene Ontology, protein families, tissue expression, and protein-protein interactions.

Conclusion

This approach was utilized to classify functionally the identified genes in discrete mitotic processes. We confirmed the identity for a subset of these genes and examined more closely their mechanical role in spindle architecture.     

The association of C-reactive protein and CRP genotype with coronary heart disease: findings from five studies with 4,610 cases amongst 18,637 participants

Background

It is unclear whether C-reactive protein (CRP) is causally related to coronary heart disease (CHD). Genetic variants that are known to be associated with CRP levels can be used to provide causal inference of the effect of CRP on CHD. Our objective was to examine the association between CRP genetic variant +1444C>T (rs1130864) and CHD risk in the largest study to date of this association.

Methods and Results

We estimated the association of CRP genetic variant +1444C>T (rs1130864) with CRP levels and with CHD in five studies and then pooled these analyses (N = 18,637 participants amongst whom there were 4,610 cases). CRP was associated with potential confounding factors (socioeconomic position, physical activity, smoking and body mass) whereas genotype (rs1130864) was not associated with these confounders. The pooled odds ratio of CHD per doubling of circulating CRP level after adjustment for age and sex was 1.13 (95%CI: 1.06, 1.21), and after further adjustment for confounding factors it was 1.07 (95%CI: 1.02, 1.13). Genotype (rs1130864) was associated with circulating CRP; the pooled ratio of geometric means of CRP level among individuals with the TT genotype compared to those with the CT/CC genotype was 1.21 (95%CI: 1.15, 1.28) and the pooled ratio of geometric means of CRP level per additional T allele was 1.14 (95%CI: 1.11, 1.18), with no strong evidence in either analyses of between study heterogeneity (I² = 0%, p>0.9 for both analyses). There was no association of genotype (rs1130864) with CHD: pooled odds ratio 1.01 (95%CI: 0.88, 1.16) comparing individuals with TT genotype to those with CT/CC genotype and 0.96 (95%CI: 0.90, 1.03) per additional T allele (I²<7.5%, p>0.6 for both meta-analyses). An instrumental variables analysis (in which the proportion of CRP levels explained by rs1130864 was related to CHD) suggested that circulating CRP was not associated with CHD: the odds ratio for a doubling of CRP level was 1.04 (95%CI: 0.61, 1.80).

Conclusions

We found no association of a genetic variant, which is known to be related to CRP levels, (rs1130864) and having CHD. These findings do not support a causal association between circulating CRP and CHD risk, but very large, extended, genetic association studies would be required to rule this out.     

Does High C-reactive Protein Concentration Increase Atherosclerosis? The Whitehall II Study

Background

C-reactive protein (CRP), a marker of systemic inflammation, is associated with risk of coronary events and sub-clinical measures of atherosclerosis. Evidence in support of this link being causal would include an association robust to adjustments for confounders (multivariable standard regression analysis) and the association of CRP gene polymorphisms with atherosclerosis (Mendelian randomization analysis).

Methodology/Principal Findings

We genotyped 3 tag single nucleotide polymorphisms (SNPs) [+1444T>C (rs1130864); +2303G>A (rs1205) and +4899T>G (rs 3093077)] in the CRP gene and assessed CRP and carotid intima-media thickness (CIMT), a structural marker of atherosclerosis, in 4941 men and women aged 50–74 (mean 61) years (the Whitehall II Study). The 4 major haplotypes from the SNPs were consistently associated with CRP level, but not with other risk factors that might confound the association between CRP and CIMT. CRP, assessed both at mean age 49 and at mean age 61, was associated both with CIMT in age and sex adjusted standard regression analyses and with potential confounding factors. However, the association of CRP with CIMT attenuated to the null with adjustment for confounding factors in both prospective and cross-sectional analyses. When examined using genetic variants as the instrument for serum CRP, there was no inferred association between CRP and CIMT.

Conclusions/Significance

Both multivariable standard regression analysis and Mendelian randomization analysis suggest that the association of CRP with carotid atheroma indexed by CIMT may not be causal.     

Differences in muscle protein synthesis and anabolic signaling in the postabsorptive state and in response to food in 65-80 year old men and women

Women have less muscle than men but lose it more slowly during aging. To discover potential underlying mechanism(s) for this we evaluated the muscle protein synthesis process in postabsorptive conditions and during feeding in twenty-nine 65-80 year old men (n = 13) and women (n = 16). We discovered that the basal concentration of phosphorylated eEF2(Thr56) was approximately 40% less (P<0.05) and the basal rate of MPS was approximately 30% greater (P = 0.02) in women than in men; the basal concentrations of muscle phosphorylated Akt(Thr308), p70s6k(Thr389), eIF4E(Ser209), and eIF4E-BP1(Thr37/46) were not different between the sexes. Feeding increased (P<0.05) Akt(Thr308) and p70s6k(Thr389) phosphorylation to the same extent in men and women but increased (P<0.05) the phosphorylation of eIF4E(Ser209) and eIF4E-BP1(Thr37/46) in men only. Accordingly, feeding increased MPS in men (P<0.01) but not in women. The postabsorptive muscle mRNA concentrations for myoD and myostatin were not different between sexes; feeding doubled myoD mRNA (P<0.05) and halved that of myostatin (P<0.05) in both sexes. Thus, there is sexual dimorphism in MPS and its control in older adults; a greater basal rate of MPS, operating over most of the day may partially explain the slower loss of muscle in older women.     

Indicators of UV Exposure in Corals and Their Relevance to Global Climate Change and Coral Bleaching

A compelling aspect of the deterioration of coral reefs is the phenomenon of coral bleaching. Through interactions with other factors such as sedimentation, pollution, and bacterial infection, bleaching can impact large areas of a reef with limited recovery, and it might be induced by a variety of stressors including temperature and salinity extremes, and ultraviolet light. Under conditions of ocean warming, often associated with calm and stratified waters, photobleaching of UV-absorb-ing chromophoric dissolved organic matter (CDOM) is increased, and penetration of both UV-B and UV-A is greatly enhanced. Indices of UV-specific effects in coral tissue are needed to test whether UV increases, associated with global climate change, are harmful to corals. To address this challenge, we have evaluated UV-specific effects in corals and have characterized factors that alter penetration of UV radiation over coral reefs. An immunoblotting assay was developed to examine UV-specific lesions (thymine dimers) in coral and zooxanthellae DNA. We observed dose-dependent increases of thymine dimers in coral (Porites porites var porites) exposed to artificial solar irradiance in a solar simulator, although effects were not strictly proportional. UV measurements were made in July 1999 at Eastern Sambo reef and nearby sites, including profiling along transects from reef to shore. Results of these analyses indicate that the coral at Eastern Sambo reef (at 3-4 meters) were receiving UV-B radiation that was equivalent to 25 to 30% of surface UV irradiance. However, the water just inside the reef in Hawk Channel (located closer to land) was considerably more opaque to UV. This water photobleached with loss of UV absorbance and fluorescence when it was exposed to simulated solar radiation. These results indicate that photobleaching of the DOM and transport of near-shore water out over the reefs might play a key role in controlling UV penetration to the reef surface.     

Hybrid Composite Coatings for Durable and Efficient Solar Hydrogen Generation under Diverse Operating Conditions

Safe and practical solar‐driven hydrogen generators must be capable of efficient and stable operation under diurnal cycling with full separation of gaseous H₂ and O₂ products. In this study, a novel architecture that fulfills all of these requirements is presented. The approach is inherently scalable and provides versatility for operation under diverse electrolyte and lighting conditions. The concept is validated using a 1 cm² triple‐junction photovoltaic cell with its illuminated photocathode protected by a composite coating comprising an organic encapsulant with an embedded catalytic support. The device is compatible with operation under conditions ranging from 1 m H₂SO₄ to 1 m KOH, enabling flexibility in selection of semiconductor, electrolyte, membrane, and catalyst. Stable operation at a solar‐to‐hydrogen conversion efficiency of >10% is demonstrated under continuous operation, as well as under diurnal light cycling for at least 4 d, with simulated sunlight. Operational characteristics are validated by extended time outdoor testing. A membrane ensures products are separated, with nonexplosive gas streams generated for both alkaline and acidic systems. Analysis of operational characteristics under different lighting conditions is enabled by comparison of a device model to experimental data.     

The Moral Lives of Laboratory Monkeys: Television and the Ethics of Care

Why do lab monkeys watch TV? This essay examines the preponderance of televisions in primate housing units based in academic research laboratories. Within such labs, television and related visual media are glossed as part-and-parcel of welfare or species-specific enrichment practices intended for research monkeys, a logic that is simultaneously historically- and ontologically-based. In many research centers, television figures prominently in the two inseparable domains of a lab monkey’s life: as a research tool employed during experiments, and in housing units where captive monkeys are said to enjoy watching TV during “down time.” My purpose is not to determine whether monkeys do indeed enjoy, or need, television; rather, I employ visual media as a means to uncover, and decipher, the moral logic of an ethics of care directed specifically at highly sentient creatures who serve as human proxies in a range of experimental contexts. I suggest that this specialized ethics of animal care materializes Mattingly’s notion of “moral laboratories” (Mattingly in Moral laboratories: family peril and the struggle for a good life, University of California Press, Berkeley, 2014), where television mediates the troublesome boundary of species difference among the simian and human subjects who cohabit laboratory worlds.     

The carbon fertilization effect over a century of anthropogenic CO2 emissions: higher intracellular CO2 and more drought resistance among invasive and native grass species contrasts with increased water use efficiency for woody plants in the US Southwest

From 1890 to 2015, anthropogenic carbon dioxide emissions have increased atmospheric CO₂ concentrations from 270 to 400 mol mol^?1. The effect of increased carbon emissions on plant growth and reproduction has been the subject of study of free‐air CO₂ enrichment (FACE) experiments. These experiments have found (i) an increase in internal CO₂ partial pressure (c_i) alongside acclimation of photosynthetic capacity, (ii) variable decreases in stomatal conductance, and (iii) that increases in yield do not increase commensurate with CO₂ concentrations. Our data set, which includes a 115‐year‐long selection of grasses collected in New Mexico since 1892, is consistent with an increased c_i as a response to historical CO₂ increase in the atmosphere, with invasive species showing the largest increase. Comparison with Palmer Drought Sensitivity Index (PDSI) for New Mexico indicates a moderate correlation with Δ¹³C (r² = 0.32, P < 0.01) before 1950, with no correlation (r² = 0.00, P = 0.91) after 1950. These results indicate that increased c_i may have conferred some drought resistance to these grasses through increased availability of CO₂ in the event of reduced stomatal conductance in response to short‐term water shortage. Comparison with C₃ trees from arid environments (Pinus longaeva and Pinus edulis in the US Southwest) as well as from wetter environments (Bromus and Poa grasses in New Mexico) suggests differing responses based on environment; arid environments in New Mexico see increased intrinsic water use efficiency (WUE) in response to historic elevated CO₂ while wetter environments see increased c_i. This study suggests that (i) the observed increases in c_i in FACE experiments are consistent with historical CO₂ increases and (ii) the CO₂ increase influences plant sensitivity to water shortage, through either increased WUE or c_i in arid and wet environments, respectively.