Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

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Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological systems. Consequently, a large number of computational methods for extracting dynamic information from such data have been developed. One example is RNA velocity analysis, in which spliced and unspliced RNA abundances are jointly modeled in order to infer a ‘direction of change’ and thereby a future state for each cell in the gene expression space. Naturally, the accuracy and interpretability of the inferred RNA velocities depend crucially on the correctness of the estimated abundances. Here, we systematically compare five widely used quantification tools, in total yielding thirteen different quantification approaches, in terms of their estimates of spliced and unspliced RNA abundances in five experimental droplet scRNA-seq data sets. We show that there are substantial differences between the quantifications obtained from different tools, and identify typical genes for which such discrepancies are observed. We further show that these abundance differences propagate to the downstream analysis, and can have a large effect on estimated velocities as well as the biological interpretation. Our results highlight that abundance quantification is a crucial aspect of the RNA velocity analysis workflow, and that both the definition of the genomic features of interest and the quantification algorithm itself require careful consideration.     

Aconitase activity and expression during the development of lemon fruit

Citrus fruits are characterized by the accumulation of high levels of citric acid in the juice sac cells and a decline in acid level toward maturation. It has been suggested that changes in mitochondrial aconitase (EC 4.2.1.3) activity affect fruit acidity. Recently, a cytosolic aconitase (cyt-Aco) homologous to mammalian iron-regulated proteins was identified in plants, leading us to re-evaluate the role of aconitase in acid accumulation. Aconitase activity was studied in 2 contrasting citrus varieties, sweet lime ( Citrus limettioides Tan., low acid) and sour lemon ( Citrus limon var. Eureka, high acid). Two aconitase isozymes were detected. One declined early in sour lemon fruit development, but was constant throughout sweet lime fruit development. Its reduction in sour lemon was associated with a decrease in aconitase activity in the mitochondrial fraction. Another isozyme was detected in sour lemon toward maturation, and was associated with an increase in aconitase activity in the soluble fraction, suggesting a cytosolic localization. The cyt-Aco was cloned from lemon juice sac cells, but in contrast to the changes in isozyme activity, its expression was constant during fruit development. We present a model, which suggests that reduction of the mitochondrial aconitase activity plays a role in acid accumulation, while an increase in the cyt-Aco activity reduces acid level toward fruit maturation.     

Environmental friendly nitrogen fertilization

With the huge intensification of agriculture and the increasing awareness to human health and natural resources sustainability, there was a shift towards the development of environmental friendly N application approaches that support sustainable use of land and sustain food production.The effectiveness of such approaches depends on their ability to synchronize plant nitrogen demand with its supply and the ability to apply favored compositions and dosages of N-species.They are also influenced by farming scale and its sophistication, and include the following key concepts: (i) Improved application modes such as split or localized ("depot") application; (ii) use of bio-amendments like nitrification and urease inhibitors and combinations of (i) and (ii); (iii) use of controlled and slow release fertilizers; (iv) Fertigation-fertilization via irrigation systems including fully automated and controlled systems; and (v) precision fertilization in large scale farming systems. The paper describes the approaches and their action mechanisms and examines their agronomic and environmental significance. The relevance of the approaches for different farming scales, levels of agronomic intensification and agro-technical sophistication is examined as well.     

Observations on the Oman Shark,Iago omanensis (Triakidae), with emphasis on the morphological and cytological changes of the oviduct and yolk sac during gestation

The shark Iago omanensis (Triakidae, Selachia) is encountered in large populations in the Gulf of Aqaba, Red Sea, at depths of 150–1,500 m. It is a placental viviparous species, reproductive all year round and giving birth to four (occasionally five) young of 170- to 180-mm total length (TL). Its distribution and morphometrics, as well as histological and cytological changes in the oviducts, were studied. The ratio of weight of the female genital organs to body weight changes from 0.7% in nongravid females to 19.8% in the final stages of pregnancy. The ripe, liberated eggs, which are 11–12 mm long and 5 mm wide, pass through the nidamental gland and settle in the uterus. The embryo attains 9- to 11-mm TL and settles on a protruding ridge of the submucosa, covered with a microvillar endometrium. At this site of attachment, a placenta is formed and the participating uterine endometrium and wall of the yolk sac undergo profound histocytological changes, forming two parts of this organ. Three forms of food provisioning occur in the growing embryos: (1) lecithotrophic, based on yolk transported from the egg to the embryonic gut via the umbilical cord; (2) mixed food provision, during which, in addition to nourishment provided via the umbilicus, food is transported across the placenta through transfer from the female blood vascular system to the embryonic yolk sac via the trophic villi of the yolk sac; and (3) histotrophic, when all yolk reserves have been used and nutrition is provided from the so-called “milk” within the yolk sac, metabolized by the trophic structures of the sac and transported by blood vessels. Despite the gradual utilization of yolk, the yolk sac mass initially increases from 0.5–1.0 cc to 2.0–2.2 cc with the addition of primary and secondary trophic villi until, during the final stages of embryogenesis, it decreases again to 1.4–1.6 cc. Neonate juveniles are 35–40 times heavier than the original eggs. J. Morphol. 236:151–165, 1998. © 1998 Wiley-Liss, Inc.     

Insights into the organization of biochemical regulatory networks using graph theory analyses

Graph theory has been a valuable mathematical modeling tool to gain insights into the topological organization of biochemical networks. There are two types of insights that may be obtained by graph theory analyses. The first provides an overview of the global organization of biochemical networks; the second uses prior knowledge to place results from multivariate experiments, such as microarray data sets, in the context of known pathways and networks to infer regulation. Using graph analyses, biochemical networks are found to be scale-free and small-world, indicating that these networks contain hubs, which are proteins that interact with many other molecules. These hubs may interact with many different types of proteins at the same time and location or at different times and locations, resulting in diverse biological responses. Groups of components in networks are organized in recurring patterns termed network motifs such as feedback and feed-forward loops. Graph analysis revealed that negative feedback loops are less common and are present mostly in proximity to the membrane, whereas positive feedback loops are highly nested in an architecture that promotes dynamical stability. Cell signaling networks have multiple pathways from some input receptors and few from others. Such topology is reminiscent of a classification system. Signaling networks display a bow-tie structure indicative of funneling information from extracellular signals and then dispatching information from a few specific central intracellular signaling nexuses. These insights show that graph theory is a valuable tool for gaining an understanding of global regulatory features of biochemical networks.     

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks

Background  

Studies of cellular signaling indicate that signal transduction pathways combine to form large networks of interactions. Viewing protein-protein and ligand-protein interactions as graphs (networks), where biomolecules are represented as nodes and their interactions are represented as links, is a promising approach for integrating experimental results from different sources to achieve a systematic understanding of the molecular mechanisms driving cell phenotype. The emergence of large-scale signaling networks provides an opportunity for topological statistical analysis while visualization of such networks represents a challenge.     

Anticonvulsant profile and teratogenic evaluation of potent new analogues of a valproic acid urea derivative in NMRI mice

BACKGROUND: Valproic acid (VPA) is used to treat epilepsy and bipolar disorders, as well as for migraine prophylaxis. However, its clinical use is limited by two life-threatening side effects: hepatotoxicity and teratogenicity. To develop a more potent and safer second-generation VPA drug, the urea derivatives of four VPA analogs (2-ethyl-3-methylpentanoyl urea, 2-ethylhexanoyl urea, 2-ethyl-4-methylpentanoyl urea, and 2-methylbutanoyl urea) were synthesized. METHODS: Four CNS-active analogs of a VPA urea derivative testedthe anticonvulsant activity in the maximal electroshock seizure test (MES) and subcutaneous metrazol seizure threshold test (scMet). Teratogenic effects of these compounds were evaluated in NMRI mice susceptible to VPA-induced teratogenicity by comparison with VPA. RESULTS: All four VPA analogs showed superior anticonvulsant activity over VPA. Compared with VPA, which induced neural tube defects (NTDs) in fetuses at 1.8 and 3.6 mmol/kg, the analog derivatives induced no NTDs at any concentration up to 4.8 mmol/kg (except for a single abnormality at 3.6 mmol/kg with 2-ethyl-3-methylpentanoyl urea). Skeletal examination also revealed that the acylurea derivatives induced vertebral and rib abnormalities in fetuses markedly less frequently than VPA. Our results confirmed that the analogue derivatives are significantly less teratogenic than VPA in NMRI mice. CONCLUSIONS: The CNS-active VPA analogs containing a urea moiety, which have better anticonvulsant potency and lack teratogenicity, are good potential candidates as second-generation VPA antiepileptic drugs. Birth Defects Res (Part B) 86:394–401, 2009. © 2009 Wiley-Liss, Inc.