Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.

Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism's complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture in Plasmodium transcriptional regulation and suggest that AP2 transcription factors may play a limited regulatory role, perhaps operating in conjunction with epigenetic factors

Routine characterization and interpretation of complex alkali feldspar intergrowths

Almost all alkali feldspar crystals contain a rich inventory of exsolution, twin, and domain microtextures that form subsequent to crystal growth and provide a record of the thermal history of the crystal and often of its involvement in replacement reactions, sometimes multiple. Microtextures strongly influence the subsequent behavior of feldspars at low temperatures during diagenesis and weathering. They are central to the retention or exchange of trace elements and of radiogenic and stable isotopes. This review is aimed at petrologists and geochemists who wish to use alkali feldspar microtextures to solve geological problems or who need to understand how microtextures influence a particular process. We suggest a systematic approach that employs methods available in most well founded laboratories. The crystallographic relationships of complex feldspar intergrowths were established by the 1970s, mainly using single-crystal X-ray diffraction, but such methods give limited information on the spatial relationships of the different elements of the microtexture, or of the mode and chronology of their formation, which require the use of microscopy. We suggest a combination of techniques with a range of spatial resolution and strongly recommend the use of orientated sections. Sections cut parallel to the perfect (001) and (010) cleavages are the easiest to locate and most informative. Techniques described are light microscopy; scanning electron microscopy using both backscattered and secondary electrons, including the use of surfaces etched in the laboratory; electron-probe microanalysis and analysis by energy-dispersive spectrometry in a scanning electron microscope; transmission electron microscopy. We discuss the use of cathodoluminescence as an auxiliary technique, but do not recommend electron-backscattered diffraction for feldspar work. We review recent publications that provide examples of the need for great care and attention to pre-existing work in microtextural studies, and suggest several topics for future work