Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r² ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.     

Mechanistic insight into the microtubule and actin cytoskeleton coupling through dynein-dependent RhoGEF inhibition

Actin-based stress fiber formation is coupled to microtubule depolymerization through the local activation of RhoA. While the RhoGEF Lfc has been implicated in this cytoskeleton coupling process, it has remained elusive how Lfc is recruited to microtubules and how microtubule recruitment moderates Lfc activity. Here, we demonstrate that the dynein light chain protein Tctex-1 is required for localization of Lfc to microtubules. Lfc residues 139-161 interact with Tctex-1 at a site distinct from the cleft that binds dynein intermediate chain. An NMR-based GEF assay revealed that interaction with Tctex-1 represses Lfc nucleotide exchange activity in an indirect manner that requires both polymerized microtubules and phosphorylation of S885 by PKA. We show that inhibition of Lfc by Tctex-1 is dynein dependent. These studies demonstrate a pivotal role of Tctex-1 as a negative regulator of actin filament organization through its control of Lfc in the crosstalk between microtubule and actin cytoskeletons.     

北极的春季:迁徙鸟类抵达的生物学

一旦鸟类抵达北极区,迁徙鸟类必须调整其生理和行为以适应不可预知的雪盖、天气、食物资源和天敌胁迫。换言之,他们必须抵抗环境干扰(压力)以便尽早迁徙到苔原上的巢区并建立领域。然后,一旦外界环境有利时,它们就立即开始繁殖。这些鸟类的繁殖有一部分是利用低雪盖区域的微生境以及雪融较快的苔原斑块(特别是在柳树Salix sp．附近)。在北极地区,地面温度在日照若干小时后急剧上升,同时无脊椎动物开始活动。风速在地面柳枝和生草丛苔原10cm下几乎减弱为零。这些条件结合在一起提供了理想的避难所,对于早春迁徙到此的雀形目鸟类尤其如此。然而,如果环境调节变得更为恶劣,这些鸟类会离开。因为与南方越冬地相比,春季北极区条件具有潜在的严酷性,所以鸟类对于应激时的肾上腺皮质反应有所调整。雄鸟到达北极地区时对于剧烈应激刺激下的肾上腺酮的分泌有所提高,并且伴随着对于负反馈敏感性的下降和肾上腺皮质层细胞对于促肾上腺皮质激素作用反应的变化。同时,肾上腺酮结合蛋白(CBG)的水平也有所提高,以至于肾上腺酮的作用在恶劣的环境条件下得到缓冲。基因组受体水平的调节,尤其是在脑和肝脏中糖皮质类固醇类似受体与肾上腺酮的低亲合性,以及肾上腺酮的非基因组水平的作用,可能是很重要的。换言之,与抵达生物学有关的激素一行为系统是高度可变的[动物学报50(6)：948-960,2004]。     

Rejoinder to Discussions on “Approval policies for modifications to machine learning‐based software as a medical device: A study of bio‐creep”

We thank the discussants for sharing their unique perspectives on the problem of designing automatic algorithm change protocols (aACPs) for machine learning‐based software as a medical device. Both Pennello et al. and Rose highlighted a number of challenges that arise in real‐world settings, and we whole‐heartedly agree that substantial extensions of our work are needed to understand if and how aACPs can be safely deployed in practice. Our work demonstrated that aACPs that appear to be harmless may allow for biocreep, even when the data distribution is assumed to be representative and stationary over time. While we investigated two solutions that protect against this specific issue, many more statistical and practical challenges remain and we look forward to future research on this topic.     

Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation

There is a groundswell of interest in using genetically engineered sensor bacteria to study gut microbiota pathways, and diagnose or treat associated diseases. Here, we computationally identify the first biological thiosulfate sensor and an improved tetrathionate sensor, both two‐component systems from marine Shewanella species, and validate them in laboratory Escherichia coli. Then, we port these sensors into a gut‐adapted probiotic E. coli strain, and develop a method based upon oral gavage and flow cytometry of colon and fecal samples to demonstrate that colon inflammation (colitis) activates the thiosulfate sensor in mice harboring native gut microbiota. Our thiosulfate sensor may have applications in bacterial diagnostics or therapeutics. Finally, our approach can be replicated for a wide range of bacterial sensors and should thus enable a new class of minimally invasive studies of gut microbiota pathways.     

Larval sites of the mosquito Aedes aegypti formosus in forest and domestic habitats in Africa and the potential association with oviposition evolution

Adaptations to anthropogenic domestic habitats contribute to the success of the mosquito Aedes aegypti as a major global vector of several arboviral diseases. The species inhabited African forests before expanding into domestic habitats and spreading to other continents. Despite a well‐studied evolutionary history, how this species initially moved into human settlements in Africa remains unclear. During this initial habitat transition, African Ae. aegypti switched their larval sites from natural water containers like tree holes to artificial containers like clay pots. Little is known about how these natural versus artificial containers differ in their characteristics. Filling this knowledge gap could provide valuable information for studying the evolution of Ae. aegypti associated with larval habitat changes. As an initial effort, in this study, we characterized the microenvironments of Ae. aegypti larval sites in forest and domestic habitats in two African localities: La Lopé, Gabon, and Rabai, Kenya. Specifically, we measured the physical characteristics, microbial density, bacterial composition, and volatile chemical profiles of multiple larval sites. In both localities, comparisons between natural containers in the forests and artificial containers in the villages revealed significantly different microenvironments. We next examined whether the between‐habitat differences in larval site microenvironments lead to differences in oviposition, a key behavior affecting larval distribution. Forest Ae. aegypti readily accepted the artificial containers we placed in the forests. Laboratory choice experiments also did not find distinct oviposition preferences between forest and village Ae. aegypti colonies. These results suggested that African Ae. aegypti are likely generalists in their larval site choices. This flexibility to accept various containers with a wide range of physical, microbial, and chemical conditions might allow Ae. aegypti to use human‐stored water as fallback larval sites during dry seasons, which is hypothesized to have initiated the domestic evolution of Ae. aegypti.