Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

<p>Abstract</p> <p>Background</p> <p>High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.</p> <p>Results</p> <p>Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of <it>S. cerevisiae </it>that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.</p

Constitutively active SARM1 variants that induce neuropathy are enriched in ALS patients

BACKGROUND: In response to injury, neurons activate a program of organized axon self-destruction initiated by the NAD METHODS: To investigate whether naturally occurring human variants might disrupt SARM1 autoinhibition and potentially contribute to risk for neurodegenerative disease, we assayed the enzymatic activity of all 42 rare SARM1 alleles identified among 8507 amyotrophic lateral sclerosis (ALS) patients and 9671 controls. We then intrathecally injected mice with virus expressing SARM1 constructs to test the capacity of an ALS-associated constitutively active SARM1 variant to promote neurodegeneration in vivo. RESULTS: Twelve out of 42 SARM1 missense variants or small in-frame deletions assayed exhibit constitutive NADase activity, including more than half of those that are unique to the ALS patients or that occur in multiple patients. There is a \u3e 5-fold enrichment of constitutively active variants among patients compared to controls. Expression of constitutively active ALS-associated SARM1 alleles in cultured dorsal root ganglion (DRG) neurons is pro-degenerative and cytotoxic. Intrathecal injection of an AAV expressing the common SARM1 reference allele is innocuous to mice, but a construct harboring SARM1 CONCLUSIONS: These results implicate rare hypermorphic SARM1 alleles as candidate genetic risk factors for ALS and other neurodegenerative conditions

SubmilliJansky Transients in Archival Radio Observations

[ABRIDGED] We report the results of a 944-epoch survey for transient sources with archival data from the Very Large Array spanning 22 years with a typical epoch separation of 7 days. Observations were obtained at 5 or 8.4 GHz for a single field of view with a full-width at half-maximum of 8.6' and 5.1', respectively, and achieved a typical point-source detection threshold at the beam center of ~300 microJy per epoch. Ten transient sources were detected with a significance threshold such that only one false positive would be expected. Of these transients, eight were detected in only a single epoch. Two transients were too faint to be detected in individual epochs but were detected in two-month averages. None of the ten transients was detected in longer-term averages or associated with persistent emission in the deep image produced from the combination of all epochs. The cumulative rate for the short timescale radio transients above 370 microJy at 5 and 8.4 GHz is 0.07 < R < 40 deg^-2 yr^-1, where the uncertainty is due to the unknown duration of the transients, 20 min < t_char < 7 days. A two-epoch survey for transients will detect 1.5 +/- 0.4 transient per square degrees above a flux density of 370 microJy. Two transients are associated with galaxies at z=0.040 and z=0.249. These may be similar to the peculiar Type Ib/c radio supernova SN 1998bw associated with GRB 980428. Six transients have no counterparts in the optical or infrared (R=27, Ks=18). The hosts and progenitors of these transients are unknown.Comment: Accepted for ApJ; full quality figures available at http://astro.berkeley.edu/~gbower/ps/rt.pd

Influence of Anthropogenic Subsidies on Movements of Common Ravens

Anthropogenic subsidies can benefit populations of generalist predators such as common ravens (ravens; Corvus corax), which in turn may depress populations of many types of species at lower-trophic levels, including desert tortoises (Gopherus agassizii) or greater sage-grouse (Centrocercus urophasianus). Management of subsidized ravens often has targeted local breeding populations that are presumed to affect species of concern and ignored “urban” populations of ravens. However, little is known about how ravens move, especially in response to the presence of anthropogenic subsidies. Therefore, subsidized ravens from distant populations that are not managed may influence local prey. To better understand this issue, we deployed global positioning system – global system for mobile communications transmitters to track movements of 19 ravens from September to December 2020 relative to 2 land cover types that provide subsidies: developed areas and cultivated crops. On average, ravens moved 41.5 km (±30.5) per day, although daily movement distances ranged from 0.13–206.1 km. Raven movement among cover types during the non-breeding season varied widely, with 100% of individuals each using land cover types that provide subsidy and other types at least once in the season. On 100% of days ravens used areas that did not provide subsidy, on 86.7% of days they used developed areas, and on 20.5% of days they used cultivated crops. Although on some days a raven would stay exclusively in areas that did not provide subsidy, there were no days in which a single raven ever stayed exclusively in developed or cultivated crops. Ravens moved shorter distances on days when they used subsidies more frequently. Further, time spent in developed areas and cultivated crops increased when ravens roosted closer to them, although this effect was greater for developed areas than for cultivated crops. Individual ravens were not associated exclusively with either of the subsidy-providing landscapes we considered, but instead all birds used both subsidized and other landscapes. Our research suggests that management of ravens during the non-breeding season and possibly during the breeding season, intended to reduce risk of predation on desert tortoises, will be most effective if conducted on a broad scale because of distances the birds travel and the lack of separation between putative “urban” and “natural” populations of ravens

Loss of Stathmin-2, a hallmark of TDP-43-associated ALS, causes motor neuropathy

TDP-43 mediates proper Stathmin-2 (STMN2) mRNA splicing, and STMN2 protein is reduced in the spinal cord of most patients with amyotrophic lateral sclerosis (ALS). To test the hypothesis that STMN2 loss contributes to ALS pathogenesis, we generated constitutive and conditional STMN2 knockout mice. Constitutive STMN2 loss results in early-onset sensory and motor neuropathy featuring impaired motor behavior and dramatic distal neuromuscular junction (NMJ) denervation of fast-fatigable motor units, which are selectively vulnerable in ALS, without axon or motoneuron degeneration. Selective excision of STMN2 in motoneurons leads to similar NMJ pathology. STMN2 knockout heterozygous mice, which better model the partial loss of STMN2 protein found in patients with ALS, display a slowly progressive, motor-selective neuropathy with functional deficits and NMJ denervation. Thus, our findings strongly support the hypothesis that STMN2 reduction owing to TDP-43 pathology contributes to ALS pathogenesis

A validated measure of adherence to antibiotic prophylaxis in children with sickle cell disease

BACKGROUND: Antibiotic prophylaxis is a mainstay in sickle cell disease management. However, adherence is estimated at only 66%. This study aimed to develop and validate a Sickle Cell Antibiotic Adherence Level Evaluation (SCAALE) to promote systematic and detailed adherence evaluation. METHODS: A 28-item questionnaire was created, covering seven adherence areas. General Adherence Ratings from the parent and one health care provider and medication possession ratios were obtained as validation measures. RESULTS: Internal consistency was very good to excellent for the total SCAALE (α=0.89) and four of the seven subscales. Correlations between SCAALE scores and validation measures were strong for the total SCAALE and five of the seven subscales. CONCLUSION: The SCAALE provides a detailed, quantitative, multidimensional, and global measurement of adherence and can promote clinical care and research

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods

Association and disparities of food insecurity and child abuse: Analysis of the National Survey of Children’s Health

Background: Child abuse is a major public health issue and is a significant risk factor for compromised development, health morbidities, and the development of mental and behavioral disorders in children. Many factors contribute to child abuse, especially family stressors. Food insecurity, a significant family stressor, likely increases the rate of child abuse while also contributing directly and indirectly to the consequences on child development and lifespan. Given the adverse effects of child abuse and food insecurity, investigating their relationship is crucial to developing mitigation strategies.Purpose: Our primary objective was to assess the relationship between child abuse and food insecurity using data from the National Survey of Children’s Health (NSCH). Given that these disproportionately affect children of different demographic groups, our study aims to identify associations amongst varying demographic factors.Methods: We conducted an observational study assessing the National Survey of Children’s Health (2016-2021) to investigate the relationship between food security and child abuse. Using survey weights provided by the NSCH, we determined population estimates and rates of children experiencing food insecurity and child abuse. We then constructed logistic regression models to assess associations, via odds ratio, between food security groups and whether the child experienced child abuse. Finally, we constructed logistic regression models, via odds ratios, to assess food security and child abuse by demographic factors.Results: While rates of food security were similar across age groups, households with lower income had higher rates of marginal or low food security, as well as homes with Black, Indigenous, multi-racial, and Hispanic children. Compared to those with high food security, the odds of children with marginal or low food security were significantly more likely to experience child abuse (AORs: 2.36, 95% CI: 2.17-2.57 and 5.24, 95% CI: 4.59-6.00, respectively). Compared to White children with high food security, Indigenous, Black, and White children were significantly more likely to experience child abuse as household food security decreased.Conclusion: Child abuse and food insecurity have a significant association, including overlapping contributory factors and disparities. Efforts to improve food insecurity through policy, community food banks, and school-based programs may secondarily reduce child abuse. To address racial/ethnic disparities, the expansion of culturally-competent, evidence-based programs to reduce food insecurity should be established, which may also reduce risk factors for child abuse