"Brain age" predicts disability accumulation in multiple sclerosis

OBJECTIVE

Neurodegenerative conditions often manifest radiologically with the appearance of premature aging. Multiple sclerosis (MS) biomarkers related to lesion burden are well developed, but measures of neurodegeneration are less well-developed. The appearance of premature aging quantified by machine learning applied to structural MRI assesses neurodegenerative pathology. We assess the explanatory and predictive power of "brain age" analysis on disability in MS using a large, real-world dataset.

METHODS

Brain age analysis is predicated on the over-estimation of predicted brain age in patients with more advanced pathology. We compared the performance of three brain age algorithms in a large, longitudinal dataset (>13,000 imaging sessions from >6,000 individual MS patients). Effects of MS, MS disease course, disability, lesion burden, and DMT efficacy were assessed using linear mixed effects models.

RESULTS

MS was associated with advanced predicted brain age cross-sectionally and accelerated brain aging longitudinally in all techniques. While MS disease course (relapsing vs. progressive) did contribute to advanced brain age, disability was the primary correlate of advanced brain age. We found that advanced brain age at study enrollment predicted more disability accumulation longitudinally. Lastly, a more youthful appearing brain (predicted brain age less than actual age) was associated with decreased disability.

INTERPRETATION

Brain age is a technically tractable and clinically relevant biomarker of disease pathology that correlates with and predicts increasing disability in MS. Advanced brain age predicts future disability accumulation.

Covariance-based vs. correlation-based functional connectivity dissociates healthy aging from Alzheimer disease

Prior studies of aging and Alzheimer disease have evaluated resting state functional connectivity (FC) using either seed-based correlation (SBC) or independent component analysis (ICA), with a focus on particular functional systems. SBC and ICA both are insensitive to differences in signal amplitude. At the same time, accumulating evidence indicates that the amplitude of spontaneous BOLD signal fluctuations is physiologically meaningful. We systematically compared covariance-based FC, which is sensitive to amplitude, vs. correlation-based FC, which is not, in affected individuals and controls drawn from two cohorts of participants including autosomal dominant Alzheimer disease (ADAD), late onset Alzheimer disease (LOAD), and age-matched controls. Functional connectivity was computed over 222 regions of interest and group differences were evaluated in terms of components projected onto a space of lower dimension. Our principal observations are: (1) Aging is associated with global loss of resting state fMRI signal amplitude that is approximately uniform across resting state networks. (2) Thus, covariance FC measures decrease with age whereas correlation FC is relatively preserved in healthy aging. (3) In contrast, symptomatic ADAD and LOAD both lead to loss of spontaneous activity amplitude as well as severely degraded correlation structure. These results demonstrate a double dissociation between age vs. Alzheimer disease and the amplitude vs. correlation structure of resting state BOLD signals. Modeling results suggest that the AD-associated loss of correlation structure is attributable to a relative increase in the fraction of locally restricted as opposed to widely shared variance.

Paternal mitochondria from an rmd-2, rmd-3, rmd-6 triple mutant are properly positioned in the C. elegans zygote

RMD-1,2,3,6 (regulator of microtubule dynamics) is a family of homologous proteins conserved between humans and C. elegans. Human RMD-3/PTPIP51 is a mitochondrial protein that tethers mitochondria to the endoplasmic reticulum. C. elegans RMD-2, 3, and 6 are expressed in sperm. To test whether paternal RMD-2, 3, 6 might redundantly tether paternal mitochondria to maternal ER at fertilization, we generated an rmd-2, rmd-3, rmd-6 triple mutant. Paternal mitochondria derived from control or triple mutant worms were concentrated in a cloud around the paternal DNA at the future posterior end of zygotes during meiosis. No significant difference was detected in the position of paternal mitochondria within the zygote nor in the position of paternal mitochondria relative to paternal DNA within the zygote. There was also no reduction in progeny viability between control and triple mutant worms.

Modeling the relative risk of SARS-CoV-2 infection to inform risk-cost-benefit analyses of activities during the SARS-CoV-2 pandemic

Risk-cost-benefit analysis requires the enumeration of decision alternatives, their associated outcomes, and the quantification of uncertainty. Public and private decision-making surrounding the COVID-19 pandemic must contend with uncertainty about the probability of infection during activities involving groups of people, in order to decide whether that activity is worth undertaking. We propose a model of SARS-CoV-2 infection probability that can produce estimates of relative risk of infection for diverse activities, so long as those activities meet a list of assumptions, including that they do not last longer than one day (e.g., sporting events, flights, concerts), and that the probability of infection among possible routes of infection (i.e., droplet, aerosol, fomite, and direct contact) are independent. We show how the model can be used to inform decisions facing governments and industry, such as opening stadiums or flying on airplanes; in particular, it allows for estimating the ranking of the constituent components of activities (e.g., going through a turnstile, sitting in one's seat) by their relative risk of infection, even when the probability of infection is unknown or uncertain. We prove that the model is a good approximation of a more refined model in which we assume infections come from a series of independent risks. A linearity assumption governing several potentially modifiable risks factors-such as duration of the activity, density of participants, and infectiousness of the attendees-makes interpreting and using the model straightforward, and we argue that it does so without significantly diminishing the reliability of the model.

A deterministic linear infection model to inform Risk-Cost-Benefit Analysis of activities during the SARS-CoV-2 pandemic

Risk-cost-benefit analysis requires the enumeration of decision alternatives, their associated outcomes, and the quantification of uncertainty. Public and private decision-making surrounding the COVID-19 pandemic must contend with uncertainty about the probability of infection during activities involving groups of people, in order to decide whether that activity is worth undertaking. We propose a deterministic linear model of SARS-CoV-2 infection probability that can produce estimates of relative risk for diverse activities, so long as those activities meet a list of assumptions, including that they do not last longer than one day. We show how the model can be used to inform decisions facing governments and industry, such as opening stadiums or flying on airplanes. We prove that the model is a good approximation of a more refined model in which we assume infections come from a series of independent risks. The linearity assumption makes interpreting and using the model straightforward, and we argue that it does so without significantly diminishing the reliability of the model.

Policy Implications of an Approximate Linear Infection Model for SARS-CoV-2

We propose a linear model of infection probability, and prove that this is a good approximation to a more refined model in which we assume infections come from a series of independent risks. We argue that the linearity assumption makes interpreting and using the model much easier, without significantly diminishing the reliability of the model.

Resolution of Murine Toxic Hepatic Injury Quantified With Ultrasound Entropy Metrics

Image-based classification of liver disease generally lacks specificity for distinguishing between acute, resolvable injury and chronic irreversible injury. We propose that ultrasound radiofrequency data acquired in vivo from livers subjected to toxic drug injury can be analyzed with information theoretic detectors to derive entropy metrics, which classify a statistical distribution of pathologic scatterers that dissipate over time as livers heal. Here we exposed 38 C57BL/6 mice to carbon tetrachloride to cause liver damage, and imaged livers in vivo 1, 4, 8, 12 and 18 d after exposure with a broadband 15-MHz probe. Selected entropy metrics manifested monotonic recovery to normal values over time as livers healed, and were correlated directly with progressive restoration of liver architecture by histologic assessment (r² ≥ 0.95, p < 0.004). Thus, recovery of normal liver microarchitecture after toxic exposure can be delineated sensitively with entropy metrics.

Network residues: The enduring impact of intra-organizational dormant ties

It is often seen as axiomatic in the social capital literature that relationships require ongoing maintenance to remain valuable. As a result, nearly all social network research has only considered relationships that are active (or recently restored to activity after a period of dormancy). Seldom considered is the impact of still-dormant, unmaintained ties that remain dormant. Using two bounded-network studies (one in a school district, one in a private company), we find consistently that still-dormant ties increase employees' organizational commitment. However, we also find that active ties can "dilute" this effect, rendering dormant ties less relevant and meaningful to individuals, or act as "preservatives" keeping dormant ties relevant and valued. In a third, vignette-based study, we find two mechanisms for the effect of dormant ties on organizational commitment: perceptions of the past (fond recollections) and future (information access). Thus, we offer a more time-oriented, layered theory of social network ties that can be activated in people's minds even when not active in practice. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

On the Stability of BOLD fMRI Correlations

Measurement of correlations between brain regions (functional connectivity) using blood oxygen level dependent (BOLD) fMRI has proven to be a powerful tool for studying the functional organization of the brain. Recently, dynamic functional connectivity has emerged as a major topic in the resting-state BOLD fMRI literature. Here, using simulations and multiple sets of empirical observations, we confirm that imposed task states can alter the correlation structure of BOLD activity. However, we find that observations of "dynamic" BOLD correlations during the resting state are largely explained by sampling variability. Beyond sampling variability, the largest part of observed "dynamics" during rest is attributable to head motion. An additional component of dynamic variability during rest is attributable to fluctuating sleep state. Thus, aside from the preceding explanatory factors, a single correlation structure-as opposed to a sequence of distinct correlation structures-may adequately describe the resting state as measured by BOLD fMRI. These results suggest that resting-state BOLD correlations do not primarily reflect moment-to-moment changes in cognitive content. Rather, resting-state BOLD correlations may predominantly reflect processes concerned with the maintenance of the long-term stability of the brain's functional organization.

A non-commutative Julia Inequality

We prove a Julia inequality for bounded non-commutative functions on polynomial polyhedra. We use this to deduce a Julia inequality for holomorphic functions on classical domains in ℂ ^d . We look at differentiability at a boundary point for functions that have a certain regularity there.

Acoustic firearm discharge detection and classification in an enclosed environment

Two different signal processing algorithms are described for detection and classification of acoustic signals generated by firearm discharges in small enclosed spaces. The first is based on the logarithm of the signal energy. The second is a joint entropy. The current study indicates that a system using both signal energy and joint entropy would be able to both detect weapon discharges and classify weapon type, in small spaces, with high statistical certainty.

Entropy vs. Energy Waveform Processing: A Comparison Based on the Heat Equation

Virtually all modern imaging devices collect electromagnetic or acoustic waves and use the energy carried by these waves to determine pixel values to create what is basically an “energy” picture. However, waves also carry “information”, as quantified by some form of entropy, and this may also be used to produce an “information” image. Numerous published studies have demonstrated the advantages of entropy, or “information imaging”, over conventional methods. The most sensitive information measure appears to be the joint entropy of the collected wave and a reference signal. The sensitivity of repeated experimental observations of a slowly-changing quantity may be defined as the mean variation (i.e., observed change) divided by mean variance (i.e., noise). Wiener integration permits computation of the required mean values and variances as solutions to the heat equation, permitting estimation of their relative magnitudes. There always exists a reference, such that joint entropy has larger variation and smaller variance than the corresponding quantities for signal energy, matching observations of several studies. Moreover, a general prescription for finding an “optimal” reference for the joint entropy emerges, which also has been validated in several studies.

Non-commutative holomorphic functions on operator domains

We characterize functions of d-tuples of bounded operators on a Hilbert space that are uniformly approximable by free polynomials on balanced open sets.

Local and distributed PiB accumulation associated with development of preclinical Alzheimer's disease

Amyloid-beta plaques are a hallmark of Alzheimer's disease (AD) that can be assessed by amyloid imaging (e.g., Pittsburgh B compound [PiB]) and summarized as a scalar value. Summary values may have clinical utility but are an average over many regions of interest, potentially obscuring important topography. This study investigates the longitudinal evolution of amyloid topographies in cognitively normal older adults who had normal (N = 131) or abnormal (N = 26) PiB scans at baseline. At 3 years follow-up, 16 participants with a previously normal PiB scan had conversion to PiB scans consistent with preclinical AD. We investigated the multivariate relationship (canonical correlation) between baseline and follow-up PiB topographies. Furthermore, we used penalized regression to investigate the added information derived from PiB topography compared to summary measures. PiB accumulation can be local, that is, a topography predicting the same topography in the future, and/or distributed, that is, one topography predicting another. Both local and distributed PiB accumulation was associated with conversion of PiB status. Additionally, elements of the multivariate topography, and not the commonly used summary scalar, correlated with future PiB changes. Consideration of the entire multivariate PiB topography provides additional information regarding the development of amyloid-beta pathology in very early preclinical AD.

Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization

Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity.

Additional results for "joint entropy of continuously differentiable ultrasonic waveforms" [J. Acoust. Soc. Am. 133(1), 283-300 (2013)]

Previous results on the use of joint entropy for detection of targeted nanoparticles accumulating in the neovasculature of MDA435 tumors [Fig. 7 of M. S. Hughes et al., J. Acoust. Soc. Am. 133, 283-300 (2013)] are extended, with sensitivity improving by nearly another factor of 2. This result is obtained using a "quasi-optimal" reference waveform in the computation of the joint entropy imaging technique used to image the accumulating nanoparticles.

Correlating structure with non-linear optical properties in xAs40Se60·(1 − x)As40S60glasses

A series ofxAs₄₀Se₆₀·(100 −x)As₄₀S₆₀glasses, wherex= 0, 25, 33, 50, 67, 75 and 100 mol% As₄₀Se₆₀, has been studied using neutron and X-ray total scattering, Raman spectroscopy and⁷⁷Se MAS-NMR.

Joint entropy of continuously differentiable ultrasonic waveforms

This study is based on an extension of the concept of joint entropy of two random variables to continuous functions, such as backscattered ultrasound. For two continuous random variables, X and Y, the joint probability density p(x,y) is ordinarily a continuous function of x and y that takes on values in a two dimensional region of the real plane. However, in the case where X=f(t) and Y=g(t) are both continuously differentiable functions, X and Y are concentrated exclusively on a curve, γ(t)=(f(t),g(t)), in the x,y plane. This concentration can only be represented using a mathematically "singular" object such as a (Schwartz) distribution. Its use for imaging requires a coarse-graining operation, which is described in this study. Subsequently, removal of the coarse-graining parameter is accomplished using the ergodic theorem. The resulting expression for joint entropy is applied to several data sets, showing the utility of the concept for both materials characterization and detection of targeted liquid nanoparticle ultrasonic contrast agents. In all cases, the sensitivity of these techniques matches or exceeds, sometimes by a factor of two, that demonstrated in previous studies that employed signal energy or alternate entropic quantities.

Mid-infrared spectral broadening in an ultrafast laser inscribed gallium lanthanum sulphide waveguide

We report the successful fabrication of mid-infrared waveguides written in a gallium lanthanum sulphide (GLS) substrate via the ultrafast laser inscription technique. Single mode guiding at 2485 nm and 3850 nm is observed. Spectral broadening spanning 1500 nm (-15dB points) is demonstrated under 3850 nm excitation.

Real-time calculation of a limiting form of the Renyi entropy applied to detection of subtle changes in scattering architecture

Previously a new method for ultrasound signal characterization using entropy H(f) was reported, and it was demonstrated that in certain settings, further improvements in signal characterization could be obtained by generalizing to Renyi entropy-based signal characterization I(f)(r) with values of r near 2 (specifically r=1.99) [M. S. Hughes et al., J. Acoust. Soc. Am. 125, 3141-3145 (2009)]. It was speculated that further improvements in sensitivity might be realized at the limit r-->2. At that time, such investigation was not feasible due to excessive computational time required to calculate I(f)(r) near this limit. In this paper, an asymptotic expression for the limiting behavior of I(f)(r) as r-->2 is derived and used to present results analogous to those obtained with I(f)(1.99). Moreover, the limiting form I(f,infinity) is computable directly from the experimentally measured waveform f(t) by an algorithm that is suitable for real-time calculation and implementation.

Experimental demonstration of spectral broadening in an all-silica Bragg fiber

We present the first report on experimental observation of nonlinear spectral broadening in an all-solid photonic band gap Bragg fiber of relatively large mode area approximately 62 microm(2). The theoretically designed Bragg fiber for this specific application was fabricated by the well known MCVD technique. Nonlinear spectral broadening was observed by launching high power femtosecond pulses of 1067 nm pump wavelength. These first results indicate that fabrication of such Bragg fibers, once perfected, should potentially serve as an alternative route for realization of supercontinuum light.

Application of Renyi entropy for ultrasonic molecular imaging

Previous work has demonstrated that a signal receiver based on a limiting form of the Shannon entropy is, in certain settings, more sensitive to subtle changes in scattering architecture than conventional energy-based signal receivers [M. S. Hughes et al., J. Acoust. Soc. Am. 121, 3542-3557 (2007)]. In this paper new results are presented demonstrating further improvements in sensitivity using a signal receiver based on the Renyi entropy.

Properties of an entropy-based signal receiver with an application to ultrasonic molecular imaging

Qualitative and quantitative properties of the finite part, H(f), of the Shannon entropy of a continuous waveform f(t) in the continuum limit are derived in order to illuminate its use for waveform characterization. Simple upper and lower bounds on H(f), based on features of f(t), are defined. Quantitative criteria for a priori estimation of the average-case variation of H(f) and log E(f), where E(f) is the signal energy of f(t) are also derived. These provide relative sensitivity estimates that could be used to prospectively choose optimal imaging strategies in real-time ultrasonic imaging machines, where system bandwidth is often pushed to its limits. To demonstrate the utility of these sensitivity relations for this application, a study designed to assess the feasibility of identification of angiogenic neovasculature targeted with perfluorocarbon nanoparticles that specifically bind to alpha(v)beta3-integrin expression in tumors was performed. The outcome of this study agrees with the prospective sensitivity estimates that were used for the two receivers. Moreover, these data demonstrate the ability of entropy-based signal receivers when used in conjunction with targeted nanoparticles to elucidate the presence of alpha(v)beta3 integrins in primordial neovasculature, particularly in acoustically unfavorable environments.

Enhanced cosmetic outcome with running horizontal mattress sutures

BACKGROUND

Cutaneous sutures should provide good wound eversion, firm closure, and cosmetically elegant results. Simple running sutures are commonly employed in cutaneous surgery but may not always be effective in achieving wound eversion.

OBJECTIVE

We compared the cosmetic results of simple running nonabsorbable sutures with running horizontal mattress sutures in primary closures of facial defects.

METHODS

Fifty-five patients with facial Mohs surgery defects appropriate for primary multilayer repair were randomized into one of two arms. Either the superior or the inferior half of the wound was closed with a running horizontal mattress suture. The other half of the wound was closed with a traditional simple running suture. At 1 week, 6 weeks, and 6 months, the cosmetically superior half of the wound, if any, was blindly determined by the investigators.

RESULTS

The running horizontal mattress suture was significantly more cosmetically pleasing than the simple running suture. Forty-seven patients completed the study. At the 6-month follow-up, 25 patients did better with the horizontal suture and 5 did worse, and with 17 patients, there was no clinically perceptible difference. The 6-week scores predicted the outcome at 6 months, but the 1-week scores did not.

CONCLUSIONS

In primary closures of the face, the running horizontal mattress suture is a cosmetically elegant alternative to a traditional running cutaneous suture. The final scar appears smoother and flatter than those produced by traditional simple running sutures.

Collagen remodeling after 585-nm pulsed dye laser irradiation: an ultrasonographic analysis

BACKGROUND AND OBJECTIVES

Nonablative dermal remodeling is an evolving technology that has generated great interest among both laser surgeons and patients. Evidence indicates that dermal collagen formation is the key mechanism of action for the nonablative techniques. We studied, with ultrasound, new collagen formation after nonablative laser irradiation.

METHODS

Ten patients with facial rhytids underwent a single treatment with a 585-nm pulsed dye laser. The patients were all female, ranging in age from 47 to 67, and were Fitzpatrick skin types I-III. Laser parameters were as follows: an energy fluence of 2.4 to 3.0 J/cm2, a pulse duration of 350 microsec, and a spot size of 5 mm with no overlap. Ultrasonographic assessments of dermal collagen were taken at baseline and at 30 and 90 days after treatment.

RESULTS

Ultrasonography demonstrated an increase in dermal collagen after a single treatment with the 585-nm pulsed dye laser. The greatest degree of neocollagenesis occurred periocularly.

CONCLUSION

A single treatment with a 585-nm pulsed dye laser appears to increase dermal collagen. This increase in dermal collagen can be assessed with noninvasive cutaneous ultrasound.

A second eIF4E protein in Schizosaccharomyces pombe has distinct eIF4G-binding properties

The eukaryotic cap-binding proteins belonging to the eIF4E family are generally involved in mediating the recruitment of ribosomes to capped mRNA. We described previously a cap-binding protein (now called eIF4E1) in Schizosaccharomyces pombe that appears to have all of the usual structural and functional attributes of an eIF4E. We have now characterised a new type of cap-binding protein (eIF4E2) from this organism, which at the amino acid sequence level, is 52% identical and 59% similar to eIF4E1. eIF4E2 is not essential in S.pombe but has some novel properties that may be related to a special function in the cell. The ratio of eIF4E2:eIF4E1 in the cell shifts in favour of eIF4E2 at higher temperatures. Despite having all of the dorsal face amino acids that have so far been associated with eIF4G binding to eIF4E1, eIF4E2 binds the eIF4E-binding domain of S.pombe eIF4G >10(2)-times weaker than eIF4E1 in vitro. The eIF4E2 cap-binding affinity is in the typical micromolar range. The results suggest that eIF4E2 is not active on the main pathway of translation initiation in fission yeast but might play a role in the adaptation strategy of this organism under specific growth conditions. Moreover, they provide insight into the molecular characteristics required for tight binding to eIF4G.

A quantitative molecular model for modulation of mammalian translation by the eIF4E-binding protein 1

Translation initiation is a key point of regulation in eukaryotic gene expression. 4E-binding proteins (4E-BPs) inhibit initiation by blocking the association of eIF4E with eIF4G, two integral components of the mRNA cap-binding complex. Phosphorylation of 4E-BP1 reduces its ability to bind to eIF4E and thereby to compete with eIF4G. A novel combination of biophysical and biochemical tools was used to measure the impact of phosphorylation and acidic side chain substitution at each potentially modulatory site in 4E-BP1. For each individual site, we have analyzed the effects of modification on eIF4E binding using affinity chromatography and surface plasmon resonance analysis, and on the regulatory function of the 4E-BP1 protein using a yeast in vivo model system and a mammalian in vitro translation assay. We find that modifications at the two sites immediately flanking the eIF4E-binding domain, Thr(46) and Ser(65), consistently have the most significant effects, and that phosphorylation of Ser(65) causes the greatest reduction in binding affinity. These results establish a quantitative framework that should contribute to understanding of the molecular interactions underlying 4E-BP1-mediated translational regulation.

The apical angle: a mathematical analysis of the ellipse

BACKGROUND

The elliptical excision is a common surgical procedure. The dermatologic literature predominantly describes an excisional geometry with a 3:1 length:width ratio and an apical angle of 30 degrees.

OBJECTIVE

To analyze the elliptical excision by applying mathematical principles and define the apical angle and its relationship to the length:width ratio.

METHODS

We examined numerous examples of elliptical excisions as presented in the dermatologic literature. We analyzed the geometry of the excisions and defined it mathematically.

RESULTS

The apical angle of a 3:1 elliptical excision is not 30 degrees. The true apical angle varies from 37 degrees to 74 degrees depending on excisional geometry.

CONCLUSION

The commonly presented apical angle of 30 degrees is incorrect and does not reflect the true apical angle of elliptical excisions.

Translation initiation: insect virus RNAs rewrite the rule book

Picorna-like insect virus RNAs direct an unorthodox form of translation initiation at a non-AUG-related codon, without involvement of initiator tRNA. This seems to involve a special type of mRNA pseudoknot structure which allows bypassing of the usual P-site-dependent mechanism.

Stabilization of eukaryotic initiation factor 4E binding to the mRNA 5'-Cap by domains of eIF4G

The eukaryotic cap-binding complex eIF4F is an essential component of the translational machinery. Recognition of the mRNA cap structure through its subunit eIF4E is a requirement for the recruitment of other translation initiation factors to the mRNA 5'-end and thereby for the attachment of the 40 S ribosomal subunit. In this study, we have investigated the mechanistic basis of the observation that eIF4E binding to the cap is enhanced in the presence of the large eIF4F subunit, eIF4G. We show that eIF4E requires access to both the mRNA 5'-cap and eIF4G to form stable complexes with short RNAs. This stabilization can be achieved using fragments of eIF4G that contain the eIF4E binding site but not the RNA recognition motifs. Full-length eIF4G is shown to induce increased eIF4E binding to cap analogues that do not contain an RNA body. Both results show that interaction of eIF4G with the mRNA is not necessary to enhance cap binding by eIF4E. Moreover, we show that the effect of binding of full-length eIF4G on the cap affinity of eIF4E can be further modulated through binding of Pab1 to eIF4G. These data are consistent with a model in which heterotropic cooperativity underlies eIF4F function.

The eukaryotic mRNA decapping protein Dcp1 interacts physically and functionally with the eIF4F translation initiation complex

Dcp1 plays a key role in the mRNA decay process in Saccharomyces cerevisiae, cleaving off the 5' cap to leave an end susceptible to exonucleolytic degradation. The eukaryotic initiation factor complex eIF4F, which in yeast contains the core components eIF4E and eIF4G, uses the cap as a binding site, serving as an initial point of assembly for the translation apparatus, and also binds the poly(A) binding protein Pab1. We show that Dcp1 binds to eIF4G and Pab1 as free proteins, as well as to the complex eIF4E-eIF4G-Pab1. Dcp1 interacts with the N-terminal region of eIF4G but does not compete significantly with eIF4E or Pab1 for binding to eIF4G. Most importantly, eIF4G acts as a function-enhancing recruitment factor for Dcp1. However, eIF4E blocks this effect as a component of the high affinity cap-binding complex eIF4E-eIF4G. Indeed, cooperative enhancement of the eIF4E-cap interaction stabilizes yeast mRNAs in vivo. These data on interactions at the interface between translation and mRNA decay suggest how events at the 5' cap and 3' poly(A) tail might be coupled.

Eukaryotic selenocysteine incorporation follows a nonprocessive mechanism that competes with translational termination

The synthesis of eukaryotic selenoproteins involves the recoding of an internal UGA codon as a site for selenocysteine incorporation. This recoding event is directed by a selenocysteine insertion sequence in the 3'-untranslated region. Because UGA also functions as a signal for peptidyl-tRNA hydrolysis, we have investigated how the rates of translational termination and selenocysteine incorporation relate to cis-acting elements in the mRNA as well as to trans-acting factors in the cytoplasm. We used cis-elements from the phospholipid glutathione peroxidase gene as the basis for this work because of its relatively high efficiency of selenocysteine incorporation. The last two codons preceding the UGA were found to exert a far greater influence on selenocysteine incorporation than nucleotides downstream of it. The efficiency of selenocysteine incorporation was generally much less than 100% but could be partially enhanced by concomitant overexpression of the tRNA(Sec) gene. The combination of two or three UGA codons in one reading frame led to a dramatic reduction in the yield of full-length protein. It is therefore unlikely that multiple incorporations of selenocysteine are processive with respect to the mode of action of the ribosomal complex binding to the UGA site. These observations are discussed in terms of the mechanism of selenoprotein synthesis and its ability to compete with termination at UGA codons.

Outcome predictors in pregnant opiate and polydrug users

A retrospective case note study of 93 women was performed in order to assess the effect of maternal factors on neonatal outcome in a group of women attending a specialist clinic for pregnant drug users. There were no significant differences in outcome for chaotic drug users compared with non-chaotic drug users, or for cocaine users compared with non-cocaine using drug users. Women who reduced their methadone dose during pregnancy delivered babies of significantly higher birth weight than those whose methadone dose remained the same or increased (median 3027 g, range 1780-3629 g vs 2645 g, range 580-3720 g). Women who abused benzodiazepines during pregnancy produced babies of significantly lower birth weight than those women who did not use benzodiazepines (median 2100 g, range 580-3520 g vs 2767 g, range 1530-3720 g). The results of this study give healthcare staff evidence to use in encouraging drug-using women to avoid benzodiazepines during pregnancy and to reduce their methadone dosage. The treatment received from a specialist clinic may mitigate against some of the other recognised effects of drug use during pregnancy.

Repressor binding to a dorsal regulatory site traps human eIF4E in a high cap-affinity state

Eukaryotic translation initiation involves recognition of the 5' end of cellular mRNA by the cap-binding complex known as eukaryotic initiation factor 4F (eIF4F). Initiation is a key point of regulation in gene expression in response to mechanisms mediated by signal transduction pathways. We have investigated the molecular interactions underlying inhibition of human eIF4E function by regulatable repressors called 4E-binding proteins (4E-BPs). Two essential components of eIF4F are the cap-binding protein eIF4E, and eIF4G, a multi-functional protein that binds both eIF4E and other essential eIFs. We show that the 4E-BPs 1 and 2 block the interaction between eIF4G and eIF4E by competing for binding to a dorsal site on eIF4E. Remarkably, binding of the 4E-BPs at this dorsal site enhances cap-binding via the ventral cap-binding slot, thus trapping eIF4E in inactive complexes with high affinity for capped mRNA. The binding contacts and affinities for the interactions between 4E-BP1/2 and eIF4E are distinct (estimated K(d) values of 10(-8) and 3x10(-9) for 4E-BP1 and 2, respectively), and the differences in these properties are determined by three amino acids within an otherwise conserved motif. These data provide a quantitative framework for a new molecular model of translational regulation.

A systematic nomenclature for new translation initiation factor genes from S. pombe and other fungi

Eukaryotic translation initiation factors and their corresponding genes have been characterized using biochemical and genetic methods from a variety of different organisms. The designations of the factors relate to their apparent roles in the biochemical process. Many gene names indicate genetic interactions with other genes or the functional attributes used to identify them. On the other hand, progress in systematic sequencing of the genomes of organisms like Saccharomyces cerevisiae and Schizosaccharomyces pombe has revealed many genes homologous to known translation initiation factor genes. The genes defined by the systematic sequencing approach are assigned numerical designations completely unrelated to their biological function. So far there have been publications on only three genes encoding translation initiation factors from Schizosaccharomyces pombe. We therefore see this an an ideal opportunity to propose a systematic and logical nomenclature for genes encoding translation initiation factor genes that can be applied to all further genes of this type that are characterized in this fission yeast.

Post-termination ribosome interactions with the 5'UTR modulate yeast mRNA stability

A novel form of post-transcriptional control is described. The 5' untranslated region (5'UTR) of the Saccharomyces cerevisiae gene encoding the AP1-like transcription factor Yap2 contains two upstream open reading frames (uORF1 and uORF2). The YAP2-type of uORF functions as a cis-acting element that attenuates gene expression at the level of mRNA turnover via termination-dependent decay. Release of post-termination ribosomes from the YAP2 5'UTR causes accelerated decay which is largely independent of the termination modulator gene UPF1. Both of the YAP2 uORFs contribute to the destabilization effect. A G/C-rich stop codon context, which seems to promote ribosome release, allows an uORF to act as a transferable 5'UTR-destabilizing element. Moreover, termination-dependent destabilization is potentiated by stable secondary structure 3' of the uORF stop codon. The potentiation of uORF-mediated destabilization is eliminated if the secondary structure is located further downstream of the uORF, and is also influenced by a modulatory mechanism involving eIF2. Destabilization is therefore linked to the kinetics of acquisition of reinitiation-competence by post-termination ribosomes in the 5'UTR. Our data explain the destabilizing properties of YAP2-type uORFs and also support a more general model for the mode of action of other known uORFs, such as those in the GCN4 mRNA.

Translational repression by human 4E-BP1 in yeast specifically requires human eIF4E as target

4E-binding proteins (4E-BPs) are believed to have important regulatory functions in controlling the rate of translation initiation in mammalian cells. They do so by binding to the mRNA cap-binding protein, eIF4E, thereby inhibiting formation of the cap-binding complex, a process essential for cap-dependent translation initiation. We have reproduced the translation-repressive function of human 4E-BP1 in yeast and find its activity to be dependent on substitution of human eIF4E for its yeast counterpart. Translation initiation and growth are inhibited when human 4E-BP1 is expressed in a strain with the human eIF4E substitution, but not in an unmodified strain. We have compared the relative affinities of human 4E-BP1 for human and yeast eIF4E, both in vitro using an m7GTP cap-binding assay and in vivo using a yeast two-hybrid assay, and find that the affinity of human 4E-BP1 for human eIF4E is markedly greater than for yeast eIF4E. Thus yeast eIF4E lacks structural features required for binding to human 4E-BP1. These results therefore demonstrate that the features of eIF4E required for binding to 4E-BP1 are distinct from those required for cap-complex assembly.

Identification and developmental expression of a 5'-3' exoribonuclease from Drosophila melanogaster

In multicellular organisms, very little is known about the role of mRNA stability in development, and few proteins involved in degradation pathways have been characterized. We have identified the Drosophila homologue of XRN1, which is the major cytoplasmic 5'-3' exoribonuclease in Saccharomyces cerevisiae. The protein sequence of this homologue (pacman) has 59% identity to S. cerevisiae XRN1 and 67% identity to the mouse homologue (mXRN1p) in certain regions. Sequencing of this cDNA revealed that it includes a trinucleotide repeat (CAG)9 which encodes polyglutamine. By directly measuring pacman exoribonuclease activity in yeast, we demonstrate that pacman can complement the yeast XRN1 mutation. Northern blots show a single transcript of approximately 5.2 kb which is abundant only in 0-8-h embryos and in adult males and females. In situ hybridization analysis revealed that the pcm transcripts are maternally derived, and are expressed at high levels in nurse cells. During early embryonic syncytial nuclear divisions, pcm transcripts are homogenously distributed. pcm mRNA is expressed abundantly and ubiquitously throughout the embryo during gastrulation, with high levels in the germ band and head structures. After germ band retraction, pcm transcripts are present at much lower levels, in agreement with the Northern results. Our experiments provide the first example of an exoribonuclease which is differentially expressed throughout development.

Posttranscriptional control of gene expression in yeast

Studies of the budding yeast Saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. Given the wide range of experimental tools applicable to S. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. This article reviews the current knowledge of the cellular components and mechanisms related to translation and mRNA decay, with the emphasis on the molecular basis for rate control and gene regulation. Recent progress in characterizing translation factors and their protein-protein and RNA-protein interactions has been rapid. Against the background of a growing body of structural information, the review discusses the thermodynamic and kinetic principles that govern the translation process. As in prokaryotic systems, translational initiation is a key point of control. Modulation of the activities of translational initiation factors imposes global regulation in the cell, while structural features of particular 5' untranslated regions, such as upstream open reading frames and effector binding sites, allow for gene-specific regulation. Recent data have revealed many new details of the molecular mechanisms involved while providing insight into the functional overlaps and molecular networking that are apparently a key feature of evolving cellular systems. An overall picture of the mechanisms governing mRNA decay has only very recently begun to develop. The latest work has revealed new information about the mRNA decay pathways, the components of the mRNA degradation machinery, and the way in which these might relate to the translation apparatus. Overall, major challenges still to be addressed include the task of relating principles of posttranscriptional control to cellular compartmentalization and polysome structure and the role of molecular channelling in these highly complex expression systems.

Cloning, expression, characterization and role of the leader sequence of a lipase from Rhizopus oryzae

A lipase from Rhizopus oryzae DSM 853 (ROL) was cloned from a chromosomal gene bank, sequenced and overexpressed in Escherichia coli. ROL and its precursors ProROL and PreProROL were purified and their pH and temperature profile was determined. In contrast to ROL, ProROL and PreProROL had considerably higher thermostability and a slightly higher pH optimum. Moreover, it could be demonstrated by in vitro experiments that the natural leader sequence of ROL is able to inhibit the folding supporting properties of the prosequence, resulting in a retardation of folding. In addition, there is strong evidence that all different lipase forms derived from Rhizopus sp. described in the literature are a result of different proteolytic processing and originate from the same gene.

Cooperative modulation by eIF4G of eIF4E-binding to the mRNA 5' cap in yeast involves a site partially shared by p20

Interaction between the mRNA 5'-cap-binding protein eIF4E and the multiadaptor protein eIF4G has been demonstrated in all eukaryotic translation assemblies examined so far. This study uses immunological, genetic and biochemical methods to map the surface amino acids on eIF4E that contribute to eIF4G binding. Cap-analogue chromatography and surface plasmon resonance (SPR) analyses demonstrate that one class of mutations in these surface regions disrupts eIF4E-eIF4G association, and thereby polysome formation and growth. The residues at these positions in wild-type eIF4E mediate positive cooperativity between the binding of eIF4G to eIF4E and the latter's cap-affinity. Moreover, two of the mutations confer temperature sensitivity in eIF4G binding to eIF4E which correlates with the formation of large numbers of inactive ribosome 80S couples in vivo and the loss of cellular protein synthesis activity. The yeast 4E-binding protein p20 is estimated by SPR to have a ten times lower binding affinity than eIF4G for eIF4E. Investigation of a second class of eIF4E mutations reveals that p20 shares only part of eIF4G's binding site on the cap-binding protein. The results presented provide a basis for understanding how cycling of eIF4E and eIF4G occurs in yeast translation and explains how p20 can act as a fine, but not as a coarse, regulator of protein synthesis.

High-energy magnetic Compton scattering experiments at ESRF

Investigations of spin densities in ferromagnetic materials using magnetic Compton scattering are reported. At the high-energy beamline ID15 at the ESRF, experiments have been carried out utilizing the high flux at very high photon energies. Energies from 60 up to 1000 keV have been used for investigations of experimental resolution, cross section, spin moments and momentum distribution. Optimized conditions are found for photon energies from 200 to 250 keV with a momentum resolution < 0.4 a.u. and a doubled magnetic effect compared with earlier measurements. In the determination of absolute spin moments multiple scattering has to be taken into account.

Test system for quantification of stop codon suppression by selenocysteine insertion in mammalian cell lines

A convenient test system was designed to investigate the efficiencies of selenocysteine inserting sequences (SECIS) responsible for the cotranslational incorporation of selenocysteine into selenoproteins of mammals. It comprises an expression vector in which the lacZ and luc genes are separated by an in-frame TGA stop codon. The coding regions are followed by a multicloning region allowing exchange of putative SECIS elements. Stop codon suppression associated with selenocysteine incorporation is readily estimated on the basis of relative luciferase activity measurements, thus providing a measure of SECIS efficiency.

The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability

Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation of post-termination events on the 5'-untranslated region (5'-UTR) directs differential control not only of translation but also of mRNA decay. Translational control is defined by two types of uORF function. The YAP1 -type uORF allows scanning 40S subunits to proceed via leaky scanning and re-initiation to the major ORF, whereas the YAP2 -type acts to block ribosomal scanning by promoting efficient termination. At the same time, the YAP2 uORFs define a new type of mRNA destabilizing element. Both post-termination ribosome scanning behaviour and mRNA decay are influenced by the coding sequence and mRNA context of the respective uORFs, including downstream elements. Our data indicate that release of post-termination ribosomes promotes largely upf -independent accelerated decay. It follows that translational termination on the 5'-UTR of a mature, non-aberrant yeast mRNA can trigger destabilization via a different pathway to that used to rid the cell of mRNAs containing premature stop codons. This route of control of non-aberrant mRNA decay influences the stress response in yeast. It is also potentially relevant to expression of the sizable number of eukaryotic mRNAs that are now recognized to contain uORFs.

VEGF and VEGF-C: specific induction of angiogenesis and lymphangiogenesis in the differentiated avian chorioallantoic membrane

The lymphangiogenic potency of endothelial growth factors has not been studied to date. This is partially due to the lack of in vivo lymphangiogenesis assays. We have studied the lymphatics of differentiated avian chorioallantoic membrane (CAM) using microinjection of Mercox resin, semi- and ultrathin sectioning, immunohistochemical detection of fibronectin and alpha-smooth muscle actin, and in situ hybridization with VEGFR-2 and VEGFR-3 probes. CAM is drained by lymphatic vessels which are arranged in a regular pattern. Arterioles and arteries are accompanied by a pair of interconnected lymphatics and form a plexus around bigger arteries. Veins are also associated with lymphatics, particularly larger veins, which are surrounded by a lymphatic plexus. The lymphatics are characterized by an extremely thin endothelial lining, pores, and the absence of a basal lamina. Patches of the extracellular matrix can be stained with an antibody against fibronectin. Lymphatic endothelial cells of differentiated CAM show ultrastructural features of this cell type. CAM lymphatics do not possess mediae. In contrast, the lymphatic trunks of the umbilical stalk are invested by a single but discontinuous layer of smooth muscle cells. CAM lymphatics express VEGFR-2 and VEGFR-3. Both the regular pattern and the typical structure of these lymphatics suggest that CAM is a suitable site to study the in vivo effects of potential lymphangiogenic factors. We have studied the effects of VEGF homo- and heterodimers, VEGF/PlGF heterodimers, and PlGF and VEGF-C homodimers on Day 13 CAM. All the growth factors containing at least one VEGF chain are angiogenic but do not induce lymphangiogenesis. PlGF-1 and PlGF-2 are neither angiogenic nor lymphangiogenic. VEGF-C is the first lymphangiogenic factor and seems to be highly chemoattractive for lymphatic endothelial cells. It induces proliferation of lymphatic endothelial cells and development of new lymphatic sinuses which are directed immediately beneath the chorionic epithelium. Our studies show that VEGF and VEGF-C are specific angiogenic and lymphangiogenic growth factors, respectively.