Network-Free Inference of Knockout Effects in Yeast

Perturbation experiments, in which a certain gene is knocked out and the expression levels of other genes are observed, constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation. Here we present a novel framework for analyzing large cohorts of gene knockout experiments and their genome-wide effects on expression levels. We devise clustering-like algorithms that identify groups of genes that behave similarly with respect to the knockout data, and utilize them to predict knockout effects and to annotate physical interactions between proteins as inhibiting or activating. Differing from previous approaches, our prediction approach does not depend on physical network information; the latter is used only for the annotation task. Consequently, it is both more efficient and of wider applicability than previous methods. We evaluate our approach using a large scale collection of gene knockout experiments in yeast, comparing it to the state-of-the-art SPINE algorithm. In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network.     

Effect of salinity on quality of various agricultural crops

Summary The effect of salinity on the quality of various agricultural crops has not yet been explored much. This information is very important to Israel due to the increasing use of saline water for irrigation. This paper reports the effect of saline irrigation water on the quality, especially the taste, of several crops. Fruits from a processing tomato cultivar exposed to various degrees of salinity had higher values for total soluble solids (TSS) and acidity than their controls. The yield of fruit after saline water irrigation is lower, but this is offset by the nigher fruit quality and its consequent higher value. Melon fruits from plants subjected to saline water scored higher in taste than their controls when the fruits were analyzed fresh. After 3–4 weeks of storage at room temperature, there was no longer any difference in taste. Even though salinity slightly increased the TSS content, this did not correlate with the taste scores. Iceberg lettuce grown with saline water did not significantly differ in taste from its control, even when the sensitive triangle taste test was used. The same was true for peanuts. Thus, for these two crops no advantage of better quality would compensate for possible lower yields. Salinity had little effect on the yield of two varieties of Chinese cabbage, but increased the frequency of tipburn.     

NADH Binds and Stabilizes the 26S Proteasomes Independent of ATP

The 26S proteasome is the end point of the ubiquitin- and ATP-dependent degradation pathway. The 26S proteasome complex (26S PC) integrity and function has been shown to be highly dependent on ATP and its homolog nucleotides. We report here that the redox molecule NADH binds the 26S PC and is sufficient in maintaining 26S PC integrity even in the absence of ATP. Five of the 19S proteasome complex subunits contain a putative NADH binding motif (GxGxxG) including the AAA-ATPase subunit, Psmc1 (Rpt2). We demonstrate that recombinant Psmc1 binds NADH via the GxGxxG motif. Introducing the ΔGxGxxG Psmc1 mutant into cells results in reduced NADH-stabilized 26S proteasomes and decreased viability following redox stress induced by the mitochondrial inhibitor rotenone. The newly identified NADH binding of 26S proteasomes advances our understanding of the molecular mechanisms of protein degradation and highlights a new link between protein homeostasis and the cellular metabolic/redox state.     

Thanatological behavior of a female Leopard (Panthera pardus fusca)

acta ethologica - We report an observation at Jhalana Leopard Reserve (JLR), Jaipur, India. On 16 March 2019, we saw a female walking up the mountain while calling her two, 4-month-old, male and...     

Migratory Masked Shrikes,Lanius nubicus staging at the desert edge: phenology,and sex- and age-related differences in body mass

Migratory Masked Shrikes (Lanius nubicus) were mist-netted during the spring and autumn migrations at Eilat, Israel. Nearly four times more shrikes were trapped during spring than in autumn. This could be explained by either the species assorting to loop migration, or a higher capture rate owing to poor body condition after crossing the Sahara in spring. In spring, no differences in phenology were observed between the sex- and age-groups. In contrast, in autumn juvenile males arrived significantly later than the rest of the population. Significant differences in wing chord length were found between the four sex and age classes (adult male, adult female, juvenile male, juvenile female) both in spring and autumn. However, significant differences in body mass were found only in autumn. In spring, in both sexes, wing length and body mass changed significantly with date of arrival. Masked Shrike in spring were lighter than in autumn. The results suggest that migration over desert is energetically costly and Eilat is a very important staging place for migratory Masked Shrikes.     

Phylogenetic,Metabolic, and Taxonomic Diversities Shape Mediterranean Fruit Fly Microbiotas during Ontogeny

The Mediterranean fruit fly (medfly) (Ceratitis capitata) lays eggs in fruits, where larvae subsequently develop, causing large-scale agricultural damage. Within its digestive tract, the fly supports an extended bacterial community that is composed of multiple strains of a variety of enterobacterial species. Most of these bacteria appear to be functionally redundant, with most strains sustaining diazotrophy and/or pectinolysis. At least some of these bacteria were shown to be vertically inherited, but colonization, structural, and metabolic aspects of the community''s dynamics have not been investigated. We used fluorescent in situ hybridization, metabolic profiling, plate cultures, and pyrosequencing to show that an initial, egg-borne, diverse community expands throughout the fly''s life cycle. While keeping “core” diazotrophic and pectinolytic functions, it also harbors diverse and fluctuating populations that express varied metabolic capabilities. We suggest that the metabolic and compositional plasticity of the fly''s microbiota provides potential adaptive advantages to the medfly host and that its acquisition and dynamics are affected by mixed processes that include stochastic effects, host behavior, and molecular barriers.     

Observations on the ixodid ticks associated with domestic ungulate animals in Jordan

Abstract

Fourteen species and subspecies of ixodid ticks, representing four genera, were collected from native sheep, goats, camels and cattle in Jordan. Haemaphysalis otophila was the most common species (48.1%) with Rhipicephalus sanguineus (15.3%), Boophilus kohlsi (14.4%) and Haemaphysalis sulcatus (11.6%) representing other common species among the 9,545 specimens examined.