Predicting the strength of UP-elements and full-length E. coli σE promoters

Predicting the location and strength of promoters from genomic sequence requires accurate sequenced-based promoter models. We present the first model of a full-length bacterial promoter, encompassing both upstream sequences (UP-elements) and core promoter modules, based on a set of 60 promoters dependent on σ(E), an alternative ECF-type σ factor. UP-element contribution, best described by the length and frequency of A- and T-tracts, in combination with a PWM-based core promoter model, accurately predicted promoter strength both in vivo and in vitro. This model also distinguished active from weak/inactive promoters. Systematic examination of promoter strength as a function of RNA polymerase (RNAP) concentration revealed that UP-element contribution varied with RNAP availability and that the σ(E) regulon is comprised of two promoter types, one of which is active only at high concentrations of RNAP. Distinct promoter types may be a general mechanism for increasing the regulatory capacity of the ECF group of alternative σ's. Our findings provide important insights into the sequence requirements for the strength and function of full-length promoters and establish guidelines for promoter prediction and for forward engineering promoters of specific strengths.     

The concentrations of urinary prostaglandins E and plasma prostaglandins F2α and E during induction of ovulation with human gonadotropins

Plasma prostaglandins F₂α and E (PGF₂α, PGE) and urinary PGE were measured in 10 women treated with human gonadotropins (HMG) and subsequently with human chorionic gonadotropins (HCG). Five women became pregnant (6 pregnancies). There was no correlation between concentrations of plasma PGF₂α or PGE and plasma estradiol or progesterone. Urinary PGE concentrations showed a positive correlation with estradiol before HCG and a negative correlation with progesterone after HCG, only in women who subsequently became pregnant.Higher urinary PGE concentrations before HCG suggest that either HMG or rising estradiol levels stimulate PGE renal production. The significant negative correlation.between urinary PGE and progesterone concentrations, after HCG, in those patients who became pregnant suggests that ovarian production of progesterone may decrease renal production of PGE.     

Contribution of ΔpH and ΔE to Photosynthesis of Chlamydomonas Reinhardtii

The contribution of two components (pH and E) of the proton motive force to photosynthesis of C. reinhardtii was studied. Valinomycin, a photophosphorylation uncoupler, decreased significantly the fast phase (related mainly to the membrane electric potential) of millisecond delayed light emission (ms-DLE) of C. reinhardtii. Nigericin, another photophosphorylation uncoupler, decreased the slow phase (related mainly to the proton gradient) and partly also the fast phase of ms-DLE. Both valinomycin and nigericin decreased the net ATP content and photosynthetic rate of C. reinhardtii, but the inhibition by nigericin was stronger than that by valinomycin. Hence both components of the proton motive force contribute to photosynthesis and although the contribution of pH is larger than that of E, the latter is not negligible in photosynthesis of C. reinhardtii.     

Variable synthesis and expression of E β and A e (E β ) Ia polypeptide chains in mice of differentH-2 haplotypes

The genetic and molecular requirements for cell-surface expression of Ia antigens precipitated by anti-I-E subregion sera have been examined. Inbred mice of thed, k, p, andr haplotypes synthesize and express on their lymphocytes the two I-region products normally found in anti-I-E-subregion immunoprecipitates, E and A_e (E ). Cells from mice of theb ands haplotypes fail to synthesize E chains but do synthesize A_e chains, which remain in the cytoplasm as partially glycosylated precursors. Cells of thef andq haplotypes fail to synthesize either the A_e or E polypeptide chains, as shown by both genetic complementation tests and analyses of total cell proteins by two-dimensional polyacrylamide gel electrophoresis. The patterns of expression of the intact E :A_e complex are consistent with the theory that both the A_e and E polypeptide chains must be present in the cells for either chain to be expressed in normal amounts on the cell surface. The implications of these observations for the genetics ofI-region-controlled functions are discussed.     

Identification and expression of the medaka inhibin βE subunit

Activin E, a member of the TGF-β super family, is a protein dimer of mature inhibin βE subunits. Recently, it is reported that hepatic activin E may act as a hepatokine that alter whole body energy/glucose metabolism in human. However, orthologues of the activin E gene have yet to be identified in lower vertebrates, including fish. Here, we cloned the medaka (Oryzias latipes) activin E cDNA from liver. Among all the mammalian inhibin β subunits, the mature medaka activin E amino acid sequence shares the highest homology with mammalian activin E. Recombinant expression studies suggest that medaka activin E, the disulfide–bound mature form of mature inhibin βE subunits, may exert its effects in a way similar to that in mammals. Although activin E mRNA is predominantly expressed in liver in mammals, it is ubiquitously expressed in medaka tissues. Since expression in the liver was enhanced after a high fat diet, medaka activin E may be associated with energy/glucose metabolism, as shown in mice and human.

     

Distribution and community structure of pelagic shrimps in the Southern Ocean between 150° E and 115° E

Summary Geographical distribution of biomass and species, community structure, and size comparisons of pelagic shrimps were investigated in the upper 1000m in the Southern Ocean between 150° E and 115° E during the austral summer (December 1985 and January 1986). The biomass ranged from 0 to 4.25 g wet weight/1000 m³ collected by the IKMT and in general tended to decrease southward. The average biomass north of the Polar Front and in the Antarctic Zone was 2.55 and 0.40 g/1000 m³, respectively. Twenty species were collected and of these eight were in the Antarctic Zone. Pelagic shrimps in the study area were assigned to four categories by their geographical distribution. The first included five upper meso-pelagic species and was restricted to the Subtropical Zone. The second included seven lower meso-pelagic species and occurred in the Subtropical and Subantarctic Zones. The third included seven lower meso-and bathy-pelagic species and was distributed from the Subtropical Zone to the Antartic Zone. The fourth category of one species was distributed from the Subantarctic Zone to the Antarctic Zone. We suggest that oceanic fronts in the study area do not constitute a distributional barrier to lower meso-and bathy-pelagic shrimps.     

Sequence and structural analysis of COVID-19 E and M proteins with MERS virus E and M proteins—A comparative study

The outbreak of SARS in 2003, MERS in 2012, and now COVID-19 in 2019 has demonstrated that Coronaviruses are capable of causing primary lethal infections in humans, and the pandemic is now a global concern. The COVID-19 belongs to the beta coronavirus family encoding 29 proteins, of which four are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins. Here we have analyzed and compared the Membrane (M) and Envelope (E) proteins of COVID-19 and MERS with SARS and Bat viruses. The sequence analysis of conserved regions of both E and M proteins revealed that many regions of COVID-19 are similar to Bat and SARS viruses while the MERS virus showed variations. The essential binding motifs found in SARS appeared in COVID-19. Besides, the M protein of COVID-19 showed a distinct serine phosphorylation site in the C-terminal domain, which looked like a catalytic triad seen in serine proteases. A Dileucine motif occurred many times in the sequence of the M protein of all the four viruses compared. Concerning the structural part, the COVID-19 E protein showed more similarity to Bat while MERS shared similarity with the SARS virus. The M protein of both COVID-19 and MERS displayed variations in the structure. The interaction between M and E proteins was also studied to know the additional binding regions. Our study highlights the critical motifs and structural regions to be considered for further research to design better inhibitors for the infection caused by these viruses.     

Structure–function analysis of hepatitis C virus envelope glycoproteins E1 and E2

Hepatitis C virus (HCV) is the leading cause of chronic liver disease in humans. The envelope proteins of HCV are potential candidates for vaccine development. The absence of three-dimensional (3D) structures for the functional domain of HCV envelope proteins [E1.E2] monomer complex has hindered overall understanding of the virus infection, and also structure-based drug design initiatives. In this study, we report a 3D model containing both E1 and E2 proteins of HCV using the recently published structure of the core domain of HCV E2 and the functional part of E1, and investigate immunogenic implications of the model. HCV [E1.E2] molecule is modeled by using aa205–319 of E1 to aa421–716 of E2. Published experimental data were used to further refine the [E1.E2] model. Based on the model, we predict 77 exposed residues and several antigenic sites within the [E1.E2] that could serve as vaccine epitopes. This study identifies eight peptides which have antigenic propensity and have two or more sequentially exposed amino acids and 12 singular sites are under negative selection pressure that can serve as vaccine or therapeutic targets. Our special interest is ₂₈₅FLVGQLFTFSPRRHW₂₉₉ which has five negatively selected sites (L286, V287, G288, T292, and G303) with three of them sequential and four amino acids exposed (F285, L286, T292, and R296). This peptide in the E1 protein maps to dengue envelope vaccine target identified previously by our group. Our model provides for the first time an overall view of both the HCV envelope proteins thereby allowing researchers explore structure-based drug design approaches.     

Localization of E1–E2 conformational transitions of sarcoplasmic reticulum Ca-ATPase by tryptic cleavage and hydrophobic labeling

Summary Tryptic peptides of Ca-ATPase in E_t and E₂ conformational states (Andersen, J. P., Jørgensen, P. L.,J. Membrane Biol. 88:187–198 (1985)) have been isolated by size exclusion high performance liquid chromatography in sodium dodecyl sulfate. This permitted unambiguous localization of a conformational sensitive tryptic split at Arg 198 by N-terminal amino acid sequence analysis. Other splits at Arg 505 and at Arg 819-Lys 825 were insensitive to E₁–E₂ transitions. Tryptic cleavage of Ca-ATPase after phosphorylation by inorganic phosphate showed that this enzyme form has a conformation similar to that of the vanadate-bound E₂ state, both in membranous and in soluble monomeric Ca-ATPase.Hydrophobic labeling of Ca-ATPase in sarcoplasmic reticulum vesicles with the photoactivable reagent trifluoromethyl-[¹²⁵I]iodophenyl-diazirine indicated that E₂ and E₂V states are more exposed to the membrane phase than E₁ and E₁P (Ca²⁺-occluded) states. The preferetial hydrophobic labeling in E₂ forms was found to be localized in the A₁ tryptic fragment.     

Pressure-induced inactivation of E. coli β-galactosidase: influence of pH and temperatur

In order to assess the feasibility of a high-pressure immunodesorption process using a β-galactosidase-anti-/3-galactosidase complex as a model, the influence of high hydrostatic pressure on the inactivation of E. coli /3-galactosidase has been investigated. The irreversible activity loss of β-galactosidase was studied as a function of pH and temperature for pressures comprised between atmospheric pressure and 500 megapascal (MPa; 1 MPa = 10 bar). This enabled us to establish a practical pressure-temperature diagram of stability for this enzyme. The stability domains determined thus appeared to be strongly dependent on the pH under atmospheric pressure of the phosphate buffer employed for pressurisation. Therefore, to interpret meaningfully this result, the influence of pressure on the pH-activity curve of β-galactosidase was investigated by using a high-pressure stopped-flow device. It appeared that the pH-activity curve of this enzyme was also reversibly affected by pressures lower than 150 MPa. An interpretation of these results in relation to the high-pressure induced changes of ionisation constants is proposed. For our practical purpose, the implications for the elaboration of a high-pressure immunodesorption process using /3-galactosidase as a tag, are discussed.     

Effect of prostaglandins E2 and F2α on in vitro development and hatching of caprine blastocysts

Prostaglandin E₂ has been shown to increase the ovine embryo hatching rate, and PGF_2α to reduce the development of rabbit, bovine, and rat embryos. The objective was to determine the effects of PGE₂ and PGF_2α on development of caprine embryos. Estrus was synchronized in does (n = 25) with medroxyprogesterone acetate (MAP) intravaginal sponges for 12 days, and superovulated with 20 units of FSH. On day 6 following estrus, embryos were flushed (n = 128) and incubated individually per well in 25 μl droplets of TCM-199 and BSA (8 mg/ml) for 6 days at 38.5 °C in a 5% CO₂: air with one of the following treatments: (1) control (0.0002% EtOH), (2) PGE₂ (7 ng/ml), (3) PGF_2α (7 ng/ml), (4) low PGE₂:high PGF_2α (3.5 ng/ml:14 ng/ml), (5) balanced PGE₂:PGF_2α (7 ng/ml:7 ng/ml), or (6) high PGE₂:low PGF_2α (14 ng/ml:3.5 ng/ml). Treatment with PGE₂ alone reduced (P < 0.05) the hatching rate (1/15; 7%). The hatching rate of embryos treated with PGF_2α alone (9/18; 50%), low PGE₂:high PGF_2α (8/16; 50%), and balanced PGE₂:PGF_2α (11/16; 69%) were similar to control (6/18; 33%). In contrast, the hatching rate was non-significantly increased (13/18; 72%) with the high PGE₂:low PGF_2α treatment. None of the treatments affected development from the morula to blastocyst stage. From the current data, it can be concluded that PGE₂ alone reduced hatching rate, and PGF_2α alone had no effect on the development of caprine embryos. High concentrations of PGE₂ with PGF_2α improved the hatching rates. Thus, uterine concentrations of PGE₂ may need to reach a threshold level to improve embryo hatching, as previously reported, while increased uterine concentrations of PGF_2α during early pregnancy would not affect development of the embryo.     

Induction of Abortion by Extra-amniotic Administration of Prostaglandins E2 and F2 α

The use of prostaglandins E₂ and F₂α, administered by extra-amniotic instillation, for the induction of abortion was studied in 94 patients in the first and second trimesters of pregnancy. Abortion was successfully induced in 87% of patients within 36 hours and in 94% within 48 hours. The mean abortion time was 22·4 hours. In 60% of patients abortion was complete.Though the differences were not statistically significant, on average multigravid patients aborted more quickly than primigravidae, while the mean abortion time in PGE₂-treated patients was less than in those receiving PGF₂α.No serious complications occurred. Some side effects were observed. Occasional vomiting was the commonest symptom but the incidence of side effects was lower than with alternative routes of administration. A leucocytosis was often noted but there were no significant instances of infection.The method has proved a safe and effective means of terminating pregnancies in the second trimester.     

Association of E/E′ and NT-proBNP with Renal Function in Patients with Essential Hypertension

Objectives

To evaluate the association of left ventricular (LV) diastolic function and N-terminal pro-brain natriuretic peptide (NT-proBNP) with renal function in essential hypertension.

Methods

LV diastolic function was estimated by the ratio of early diastolic velocities (E) from transmitral inflow to early diastolic velocities (E′) of tissue Doppler at mitral annulus (septal corner); NT-proBNP was measured in 207 hypertensive patients (mean age 56±14 years). The subjects were classified into 3 groups: E/E′≤10 group (n = 48), 10<E/E′≤15 group (n = 109) and E/E′>15 group (n = 50). The renal function was estimated by glomerular filtration rate (GFR) with ^99mTc-DTPA. GFR from 30 to 59 ml/min/1.73 m² was defined as Stage 3 chronic kidney disease (CKD). GFR was also estimated using the modified MDRD equation. Albuminuria was defined by urinary albumin/creatinine ratio (UACR).

Results

GFR was lower and UACR was higher in E/E′ >15 group than in 10< E/E′ ≤15 group or E/E′ ≤10 group (p<0.0001), GFR was significantly negative and UACR was positive correlated with E/E′ and NT-proBNP (p<0.0001). In multivariate stepwise linear analysis, GFR had significant correlation with age (p = 0.001), gender (p = 0.003), E/E′ (p = 0.03), lgNT-proBNP (p = 0.001) and lgUACR (p = 0.01), while eGFR had no significant correlation with E/E′ or lgNT-proBNP. Multivariate logistic regression analysis, adjusted for potential confounding factors, showed that participants in E/E′>15 group were more likely to have Stage 3 CKD compared with those in E/E′≤10 group with an adjusted odds ratio of 8.31 (p = 0.0036).

Conclusions

LV diastolic function, assessed with E/E′ and NT-proBNP is associated with renal function in essential hypertension.     

Contractile responses of longitudinal and circular smooth muscle of the canine stomach to prostaglandins E and F2α

Muscle strips were excised from the circular and longitudinal layers of the fundus, corpus and antrum, and from the inner portion of the pyloric ring. In general prostaglandin(PG)F₂α as well as PGE₁ and PGE₂ stimulated the longitudinal muscle. However, there were remarkable regional differences. The sensitivity to PGs was greatest in the fundus and corpus (threshold near 10⁻¹⁰ mol/1) and only weak in antrum (threshold 5·10⁻⁸ to 10⁻⁷ mol/1). In longitudinal antrum strips acetylcholine induced a combined phasic-tonic response, whereas PGs produced purely phasic responses. The effects of PGF_2α and PGE on the circular layer were complex. PGF_2α produced excitatory responses in circular fundus and corpus similar to those in the longitudinal layer of the same regions. PGE produced dual responses in circular fundus (excitation at low concentration and strong inhibition at concentration of 10⁻⁷ mol/1). In circular corpus PGE induced pure inhibition (threshold near 10⁻⁹ mol/1). In circular antrum and inner pylorus both PGE and PGF_2α produced inhibition of the phasic activity (threshold 10⁻⁸ to 10⁻⁷ for antrum and 10⁻⁹ mol/1 for inner pylorus). These effects of PGs appeared in the presence of adrenergic and cholinergic blocking agents as well as of tetrodotoxin and were therefore, direct effects on smooth muscle. Indomethacin (10⁻⁷–10⁻⁶ mol/1) suppressed spontaneous tone of the fundus and corpus and increased phasic activity of inner pylorus. This indicates that endogenous PG synthesis may be involved in the control of spontaneous activity in gastric muscle.     

Effect of prostaglandins F2α and E2 on sensitivity of rabbit cortical neurons to acetylcholine and noradrenalin

The effect of prostaglandins F₂ and E₂ on unit activity and sensitivity of somatosensory cortical neurons of rabbits to acetylcholine and noradrenalin was investigated by microiontophoresis. Prostaglandin F₂ predominantly inhibited, whereas E₂ increased the spike activity of the neurons. F₂ usually modified the sensitivity of the neurons to acetylcholine, E₂ to noradrenalin. The influence of F₂ on the excitatory effects of acetylcholine, and of E₂ on the inhibitory effects of noradrenalin as a rule was characterized by weakening of the action of the mediators or a change in the sign of the initial responses. It is suggested that prostaglandins of the F group participate in cholinergic, and those of the E group in adrenergic transmission. The prostaglandins studied evidently exert their action through selective inhibition of the activity of adenylate or guanylate cyclases, leading to a decrease in the synthesis of secondary transmitters, namely cyclic AMP and cyclic GMP.B. K. Anokhin Research Institute of Normal Physiology, Academy of Medical Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 12, No. 3, pp. 239–245, May–June, 1980.     

Toxic and repulsive effects of spray, ‘per os’ and systemic applications of destruxin E to aphids

Repellent, aphicidal, destruxin E has interesting properties towards aphids for which some important differences of susceptibility between species have been observed. M. persicae is sensitive to this molecule which kills 50% of the individuals stinging a leaf on which destruxin has been deposited at the rate of 0.4 g/cm². Feeding by the cabbage aphid, B. brassicae, is decreased by 8.8 ppm of destruxin E in the sap, whereas R. padi is resistant to inhibition of feeding activity.     

Contribution of charged and polar residues for the formation of the E1–E2 heterodimer from Hepatitis C Virus

The transmembrane domains of the envelope glycoprotein E1 and E2 have crucial multifunctional roles in the biogenesis of hepatitis C virus. We have performed molecular dynamics simulations to investigate a structural model of the transmembrane segments of the E1–E2 heterodimer. The simulations support the key role of the Lys370–Asp728 ion pair for mediating the E1–E2 heterodimerization. In comparison to these two residues, the simulation results also reveal the differential effect of the conserved Arg730 residue that has been observed in experimental studies. Furthermore, we discovered the formation of inter-helical hydrogen bonds via Asn367 that stabilize dimer formation. Simulations of single and double mutants further demonstrate the importance of the ion-pair and polar interactions between the interacting helix monomers. The conformation of the E1 fragment in the simulation of the E1–E2 heterodimer is in close agreement with an NMR structure of the E1 transmembrane segment. The proposed model of the E1–E2 heterodimer supports the postulated cooperative insertion of both helices by the translocon complex into the bilayer.     

On the origin and characteristics of noise-induced Lévy walks of E. coli

Lévy walks as a random search strategy have recently attracted a lot of attention, and have been described in many animal species. However, very little is known about one of the most important issues, namely how Lévy walks are generated by biological organisms. We study a model of the chemotaxis signaling pathway of E. coli, and demonstrate that stochastic fluctuations and the specific design of the signaling pathway in concert enable the generation of Lévy walks. We show that Lévy walks result from the superposition of an ensemble of exponential distributions, which occurs due to the shifts in the internal enzyme concentrations following the stochastic fluctuations. With our approach we derive the power-law analytically from a model of the chemotaxis signaling pathway, and obtain a power-law exponent μ ≈ 2.2, which coincides with experimental results. This work provides a means to confirm Lévy walks as natural phenomenon by providing understanding on the process through which they emerge. Furthermore, our results give novel insights into the design aspects of biological systems that are capable of translating additive noise on the microscopic scale into beneficial macroscopic behavior.