IgGeneUsage: differential gene usage in immune repertoires

Summary Decoding the properties of immune repertoires is key to understanding the adaptive immune response to challenges such as viral infection. One important quantitative property is differential usage of Ig genes between biological conditions. Yet, most analyses for differential Ig gene usage are performed qualitatively or with inadequate statistical methods. Here we introduce IgGeneUsage, a computational tool for the analysis of differential Ig gene usage. IgGeneUsage employs Bayesian inference with hierarchical models to analyze complex gene usage data from high-throughput sequencing experiments of immune repertoires. It quantifies differential Ig gene usage probabilistically and avoids some common problems related to the current practice of null-hypothesis significance testing. Availability and implementation IgGeneUsage is an R-package freely available as part of Bioconductor at: https://bioconductor.org/packages/IgGeneUsage/. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Recent development of PeakForce Tapping mode atomic force microscopy and its applications on nanoscience

Nanoscience is a booming field incorporating some of the most fundamental questions concerning structure, function, and applications. The cutting-edge research in nanoscience requires access to advanced techniques and instrumentation capable of approaching these unanswered questions. Over the past few decades, atomic force microscopy (AFM) has been developed as a powerful platform, which enables in situ characterization of topological structures, local physical properties, and even manipulating samples at nanometer scale. Currently, an imaging mode called PeakForce Tapping (PFT) has attracted more and more attention due to its advantages of nondestructive characterization, high-resolution imaging, and concurrent quantitative property mapping. In this review, the origin, principle, and advantages of PFT on nanoscience are introduced in detail. Three typical applications of this technique, including high-resolution imaging of soft samples in liquid environment, quantitative nanomechanical property mapping, and electrical/electrochemical property measurement will be reviewed comprehensively. The future trends of PFT technique development will be discussed as well.

Cycology – what has been learnt from previous real estate cycles?

Purpose The purpose of this paper is to look at the lessons learnt from the previous real estate cycles based on a sample of investors, occupiers and academics and seek to understand the practical challenges the industry faces in the current cycle. Design/methodology/approach The paper summarises the results of qualitative research and interviews conducted and analysed by BNP Paribas Real Estate and Ipsos MORI. Findings The paper considers the crisis of 2008, its impact on performance, lessons learnt by the industry as a result and the future challenges. Whilst the industry felt well prepared to withstand future uncertainty and change, there was concern that subsequent generations of industry professionals will not be well equipped to deal with the pace and magnitude of change. Practical implications This is a practical study that seeks to place a greater emphasis on the drivers of market sentiment rather than focussing on quantitative forecasts. Originality/value There is much attention given to quantitative property market forecasts; however, there seems to be little appreciation of the need to evolve our process in today’s fast paced, structurally changing market which will behave differently to how it has in the past. Economic forecasts have received much criticism recently and these provide the basis for property market forecasts. The consideration of sentiment and the qualitative aspect of the future drivers of performance have never been so critical.

Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice

Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant’s response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.