Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

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Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research

The contribution of balanced chromosomal rearrangements to complex disorders remains unclear because they are not detected routinely by genome-wide microarrays and clinical localization is imprecise. Failure to consider these events bypasses a potentially powerful complement to single nucleotide polymorphism and copy-number association approaches to complex disorders, where much of the heritability remains unexplained. To capitalize on this genetic resource, we have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequencing. For rearrangements already mapped regionally by karyotyping and fluorescence in situ hybridization, a targeted approach enabled capture and sequencing of multiple breakpoints simultaneously. Importantly, this strategy permitted capture and unique alignment of up to 97% of repeat-masked sequences in the targeted regions. Genome-wide analyses estimate that only 3.7% of bases should be routinely omitted from genomic DNA capture experiments. Illustrating the power of these approaches, the rearrangement breakpoints were rapidly defined to base pair resolution and revealed unexpected sequence complexity, such as co-occurrence of inversion and translocation as an underlying feature of karyotypically balanced alterations. These findings have implications ranging from genome annotation to de novo assemblies and could enable sequencing screens for structural variations at a cost comparable to that of microarrays in standard clinical practice.     

Soil respiration in an irrigated oasis agroecosystem: linking environmental controls with plant activities on hourly,daily and monthly timescales

Aim

To investigate the responses of different components of soil respiration to environmental factors at different timescales in a vineyard ecosystem.

Methods

The trenching method was used to separate total soil respiration (TSR) into autotrophic respiration (AR) and heterotrophic respiration (HR). Soil respiration rates were measured by an LI-8100 automated flux system.

Results

On the hourly scale, there were contrasting responses in TSR, HR and AR to soil temperature at 5 cm (ST₅), with clockwise hysteresis loop responses of TSR and HR to ST₅ but a counterclockwise hysteresis loop between AR and ST₅. The daily TSR didn’t exponentially response to ST₅ during the growing season. On the monthly scale, the relationship between TSR and ST₅ showed a counterclockwise hysteresis loop. Meanwhile, the diel respiration peak lagged the peak of gross primary productivity (GPP), but the monthly peak of TSR preceded the monthly peak of GPP. The daily TSR and the daily soil water content at 5 cm (SWC₅) in different months showed a quadratic relationship, but there was an exponential correlation between the monthly TSR and the monthly SWC₅.

Conclusions

The relationship between soil respiration and environmental factors derived for a specific timescale cannot be directly applied to other timescales.

     

Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency

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