How essential are nonessential genes?

Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts in rich media. Comparing 55 genomes of Firmicutes and Gamma-proteobacteria to identify the genes which, while persistent among genomes, do not lead to a lethal phenotype when inactivated, we show that the characteristics of persistence, conservation, expression, and location are shared between persistent nonessential (PNE) genes and experimentally essential genes. PNE genes show an overrepresentation of genes related to maintenance and stress response. This outlines the limits of current experimental techniques to define gene essentiality and highlights the essential role of genes implicated in maintenance which, although dispensable for growth, are not dispensable from an evolutionary point of view. Firmicutes and Gamma-proteobacteria are mostly differing in the construction of the cell envelope, DNA replication and proofreading, and RNA degradation. In addition to suggesting functions for persistent genes that had until now resisted identification, we show that these genes have many characters in common with experimentally identified essential genes. They should then be regarded as truly essential genes.     

Do essential genes evolve slowly?

Approximately two thirds of all knockouts of individual mouse genes give rise to viable fertile mice. These genes have thus been termed 'non-essential' in contrast to 'essential' genes, the knockouts of which result in death or infertility. Although non-essential genes are likely to be under selection that favours sequence conservation [1], it is predicted that they are less subject to such stabilising selection than essential genes, and hence evolve faster [2]. We have addressed this issue by analysing the molecular evolution of 108 non-essential and 67 essential genes that have been sequenced in both mouse and rat. On preliminary analysis, the non-essential genes appeared to be faster evolving than the essential ones. We found, however, that the non-essential class contains a disproportionate number of immune-system genes that may be under directional selection (that is, selection favouring change) because of host-parasite coevolution. After correction for this bias, we found that the rate at which genes evolve does not correlate with the severity of the knockout phenotype. This was corroborated by the finding that, whereas neuron-specific genes have significantly lower rates of change than other genes, essential and non-essential neuronal genes have comparable rates of evolution. Our findings most probably reflect strong selection acting against even very subtle deleterious phenotypes, and indicate that the putative involvement of directional selection in host-parasite coevolution and gene expression within the nervous system explains much more of the variance in rates of gene evolution than does the knockout phenotype.     

Is chromium a trace essential metal?

If chromium is an essential metal it must have a specific role in an enzyme or cofactor, and a deficiency should produce a disease or impairment of function. To date, no chromium-containing glucose tolerance factor has been characterized, the purpose of the low-molecular-weight chromium-binding protein is questionable, and no direct interaction between chromium and insulin has been found. Furthermore, chromium3+ is treated like the toxic metals arsenic, cadmium, lead and mercury in animals. Chromium3+ may be involved in chromium6+-induced cancers because chromium6+ is converted to chromium3+ in vivo, and chromium3+ is genotoxic and mutagenic. Although there is no direct evidence of chromium deficiencies in humans, dietary supplements exist to provide supraphysiological doses of absorbable chromium3+. Chromium3+ may act clinically by interfering with iron absorption, decreasing the high iron stores that are linked to diabetes and heart disease. If so, this would make chromium3+ a pharmacological agent, not an essential metal.     

Rubidium—A possible essential trace element

The rubidium content of whole blood was estimated by instrumental neutron activation analysis. In 46 healthy children it amounts to {ie193-1} g/g dry weight. There was no difference between the values found for infants, toddlers, and school children. In 29 dietetically treated patients with phenylketonuria and maple-syrup-urine disease the values were significantly lower than in healthy children. During the first three months of diet therapy the rubidium levels remained in the lower range of the normal values, decreasing to about 60% of the mean of normal values later on. With increasing length of diet therapy these values tended to decrease. It remains questionable whether these decreased levels reflect only an induced biochemical phenomenon without biological importance, or whether they are the first signs of a deficiency syndrome.     

HP1 proteins--what is the essential interaction?

There are three mammalian HP1 genes, Cbx5 (encoding HP1alpha), Cbx1 (encoding HP1beta) and Cbx3 (encoding HP1gamma). Despite their high degree of sequence homology mutational analysis has revealed different phenotypes indicating that they possess different functions. Notably, the Cbx1 mutation is lethal in its homozygous condition. The Cbx1 null phenotype is therefore more severe than the Suv(3)9h1/h2 double-mutant mouse, indicating that the essential function of the Cbx1 gene product, HP1beta, is likely to lie outside its interaction with the heterochromatic H3K9me3 determinant of the "histone code" imposed by the Suv(3)9h1/h2 HMTases. Comparisons of HPI mutants in flies and fungi with corresponding mutations in Suv(3)9 genes show that HP1 mutations are invariably more severe than mutation in Suv(3)9 genes. The implications of these data for HP1 function are discussed.     

Is aluminum an essential element for life?

Aluminum is proposed to be an essential element for life based on the idea that the chemical composition of living organisms must reflect to some extent the composition of the environment in which they evolved.     

Is it true that essential tremor affects sleep? A comparison between young essential tremor patients and normal controls

Essential tremor (ET) is the most common movement disorder and cause of functional disability. ET is known as a monosymptomatic, pure motor system disease. This interpretation of ET has been questioned in the last decade. Non-motor symptoms have added to the definition of the disease. In autopsy studies, it has been reported that Lewy bodies are common in the locus coeruleus, which is known to have an active role in sleep. Previous research about sleep in ET has studied older patients. Sleep disturbances are common in older adults. Our study focused on younger patients who had the disease for a shorter period of time. 40 patients (24.9 ± 7.0 years old) and 28 controls were recruited for the study. Sleep quality was evaluated with the Pittsburg Sleep Quality Index (PSQI). Excessive daytime sleepiness (EDS) was evaluated with the Epworth Sleepiness Scale (ESS). For assessing the possible impact of depression and anxiety on sleep we used the Beck Depression Inventory (BDI), and the Beck Anxiety Scale (BAS). We ruled out other possible causes of tremor. Tremor was evaluated using the Fahn Tolosa Marin Tremor Rating Scale (FTM-TRS). We concluded that although ET patients had bad sleep quality, this might be associated with increased anxiety levels. Mean ESS scores were higher in the patient group, but this was not statistically significant.

     

CK2α is essential for embryonic morphogenesis

CK2 is a highly conserved serine-threonine kinase involved in biological processes such as embryonic development, circadian rhythms, inflammation, and cancer. Biochemical experiments have implicated CK2 in the control of several cellular processes and in the regulation of signal transduction pathways. Our laboratory is interested in characterizing the cellular, signaling, and molecular mechanisms regulated by CK2 during early embryonic development. For this purpose, animal models, including mice deficient in CK2 genes, are indispensable tools. Using CK2α gene-deficient mice, we have recently shown that CK2α is a critical regulator of mid-gestational morphogenetic processes, as CK2α deficiency results in defects in heart, brain, pharyngeal arch, tail bud, limb bud, and somite formation. Morphogenetic processes depend upon the precise coordination of essential cellular processes in which CK2 has been implicated, such as proliferation and survival. Here, we summarize the overall phenotype found in CK2α (-/- ) mice and describe our initial analysis aimed to identify the cellular processes affected in CK2α mutants.     

How to identify essential genes from molecular networks?

Background  

The prediction of essential genes from molecular networks is a way to test the understanding of essentiality in the context of what is known about the network. However, the current knowledge on molecular network structures is incomplete yet, and consequently the strategies aimed to predict essential genes are prone to uncertain predictions. We propose that simultaneously evaluating different network structures and different algorithms representing gene essentiality (centrality measures) may identify essential genes in networks in a reliable fashion.     

Is the iron an essential nutrient for enterococci?

Enterococci were considered as not requiring iron. The aim of study was evaluation of relationship between enterococci and iron. This study examined these relationships in a 71 strains belonging to two species--Enterococcus faecalis and Enterococcus faecium, which are often isolated from human infections. The iron is an essential nutrient for enterococci. Demonstrated that iron--regardless of the concentration in the medium--is collected during growth. Iron deficiency in the nutrient medium resulted in changes in the kinetics of growth of enterococci. Inhibiting the growth of enterococci by iron chelators and lack of inhibition are further proof of this demand for iron bacteria. Enterococci have the ability to acquire this important element of its connections with natural and synthetic chetators with different strength of chemical bonding and structure. Bacteria of the genus Enterococcus have a natural resistance to many antimicrobial agents. In the hospital environment can easily acquire resistance genes to many other classes of antimicrobial compounds. For these reasons, treatment of enterococal infections poses more difficulties. Inhibition of iron uptake in enterococci can be helpful in reducing and combating enterococal infections.     

Is the fur gene of Rhizobium leguminosarum essential?

Using primers corresponding to conserved regions of the bacterial regulatory gene fur, a homologue of this gene from the genome of Rhizobium leguminosarum biovar viciae, the nitrogen-fixing symbiont of peas, was isolated and sequenced. The fur gene is normally expressed constitutively, independent of the presence of Fe in the medium, but in one Rhizobium strain it was transcribed at a low level. Attempts to isolate a fur knockout mutant failed, suggesting that the gene is essential for free-living growth. In other bacteria, certain fur mutations confer manganese resistance; however, none of the manganese-resistant mutants of R. leguminosarum which we isolated was corrected by the cloned fur gene. When the cloned R. leguminosarum fur gene was introduced into a fur mutant of Escherichia coli, it caused some Fe-dependent reduction in the amount of siderophore, indicating that it can function heterologously.     

Laminin α1 is essential for mouse cerebellar development

Laminin α1 (Lama1), which is a subunit of laminin-1 (laminin-111), a heterotrimeric ECM protein, is essential for embryonic development and promotes neurite outgrowth in culture. Because the deletion of Lama1 causes lethality at early embryonic stages in mice, the in vivo role of Lama1 in neural development and functions has not yet been possible to determine. In this study, we generated conditional Lama1 knockout (Lama1(CKO)) mice in the epiblast lineage using Sox2-Cre mice. These Lama1(CKO) mice survived, but displayed behavioral disorders and impaired formation of the cerebellum. Deficiency of Lama1 in the pial basement membrane of the meninges resulted in defects in the conformation of the meninges. During cerebellar development, Lama1 deficiency also caused a decrease in the proliferation and migration of granule cell precursors, disorganization of Bergmann glial fibers and endfeet, and a transient reduction in the activity of Akt. A marked reduction in numbers of dendritic processes in Purkinje cells was observed in Lama1(CKO) mice. Together, these results indicate that Lama1 is required for cerebellar development and functions.     

We-intentionality: an essential element in understanding human culture?

Culture is a powerful cause of human behavior, yet there have been few attempts to synthesize the biological and social sciences in order to provide an explanation of culture and hence to lay the foundations for a comprehensive human science. This essay explores one possible way of doing this by outlining the likely psychological mechanisms that give rise to the unique human capacity for creating social reality. The core assumption is that "we-intentionality," which is key to understanding social constructions, can and must be linked to specific evolved psychological traits, and hence placed within a neuroscience perspective.     

Developing essential hypertension: a syndrome involving ANF deficiency?

The pathogenesis of essential hypertension may possibly involve a deficiency in, or a decreased response to, endogenous vasodilator and natriuretic factor(s). Searching for hereditary or familial defects, it is plausible to evaluate blood pressure (BP) regulating factors in (yet) normotensive offspring of hypertensive parents (OHyp), some of whom are in fact in a stage of prehypertension. Studies by our group demonstrated that compared with healthy offspring of normotensive parents, OHyp have plasma atrial natriuretic (ANF) factor levels that are unaltered on a low salt intake but often fail to increase normally in response to a high salt intake. Plasma levels of cyclic GMP, the presumed second messenger of ANF, also may tend to be decreased in certain OHyp. On the other hand, renal excretory responses of cyclic GMP and electrolytes to ANF infused in "physiological" dose were unchanged in some OHyp tested so far. In borderline to moderate, uncomplicated essential hypertension, plasma ANF levels are often "normal." This may be inappropriately low relative to the existing BP, although the relationship of circulating ANF to atrial pressures in essential hypertension remains to be clarified. A conversion to higher plasma ANF values may occur with cardiac complications such as left ventricular hypertrophy, enlargement, dysfunction, or overt heart failure. Acute or short-term elevation of circulating ANF within the physiological and pathophysiological range by ANF infusion produces an exaggerated natriuresis and lowers BP in essential hypertensive patients. We postulate a syndrome of ANF deficiency, characterized by an impaired response of circulating ANF to high salt intake and by low cyclic GMP levels in certain yet normotensive offspring of essential hypertensive parents and by inappropriately "normal" plasma ANF in some patients with uncomplicated essential hypertension. At the stage of prehypertension, a disturbance in the ANF - cyclic GMP pathway may be expressed primarily at the circulatory rather than at the renal level. Hypertension-prone humans also tend to have an exaggerated vascular reactivity to norepinephrine. Whether the two disturbances may be interrelated is presently unknown. Both defects may potentially predispose to the development of essential hypertension. Relative ANF deficiency, an enhanced natriuretic response to ANF, and a sustained antihypertensive effect of infused ANF may represent a rational basis for treatment of essential hypertension with agents that activate the ANF system.