Pathogenic TFG Mutations Underlying Hereditary Spastic Paraplegia Impair Secretory Protein Trafficking and Axon Fasciculation

Length-dependent axonopathy of the corticospinal tract causes lower limb spasticity and is characteristic of several neurological disorders, including hereditary spastic paraplegia (HSP) and amyotrophic lateral sclerosis. Mutations in Trk-fused gene (TFG) have been implicated in both diseases, but the pathomechanisms by which these alterations cause neuropathy remain unclear. Here, we biochemically and genetically define the impact of a mutation within the TFG coiled-coil domain, which underlies earlyonset forms of HSP. We find that the TFG (p.R106C) mutation alters compaction of TFG ring complexes, which play a critical role in the export of cargoes from the endoplasmic reticulum (ER). Using CRISPR-mediated genome editing, we engineered human stem cells that express the mutant form of TFG at endogenous levels and identified specific defects in secretion from the ER and axon fasciculation following neuronal differentiation. Together, our data highlight a key role for TFG-mediated protein transport in the pathogenesis of HSP.

Slosarek et al. demonstrate that pathological mutations in TFG, which underlie various forms of neurodegenerative disease, impair secretory protein transport from the endoplasmic reticulum and compromise the ability of axons to self-associate. These findings highlight a critical function for the early secretory pathway in neuronal maintenance.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase

Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.

Conformational flexibility in the enterovirus RNA replication platform

A presumed RNA cloverleaf (5'CL), located at the 5'-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem-loop B (SLB) and stem-loop D (SLD), the two largest stem-loops within the 5'CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5'CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB and SLD into close contact, a geometry that creates an extensive accessible major groove surface, and permits interaction between the proteins that target each stem-loop.

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression.

Brr6 plays a role in gene recruitment and transcriptional regulation at the nuclear envelope

Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes, but the mechanisms involved are not well understood. We show that brr6-1, a mutant of the essential yeast envelope transmembrane protein Brr6p, impairs normal positioning and expression of the PAB1 and FUR4-GAL1,10,7 loci. Similarly, expression of a dominant negative nucleoplasmic Brr6 fragment in wild-type cells reproduced many of the brr6-1 effects. Histone chromatin immunoprecipitation (ChIP) experiments showed decreased acetylation at the key histone H4K16 residue in the FUR4-GAL1,10,7 region in brr6-1. Importantly, blocking deacetylation significantly suppressed selected brr6-1 phenotypes. ChIPseq with FLAG-tagged Brr6 fragments showed enrichment at FUR4 and several other genes that showed striking changes in brr6-1 RNAseq data. These associations depended on a Brr6 putative zinc finger domain. Importantly, artificially tethering the GAL1 locus to the envelope suppressed the brr6-1 effects on GAL1 and FUR4 expression and increased H4K16 acetylation between GAL1 and FUR4 in the mutant. Together these results argue that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope.

Using Hydrogen-Deuterium Exchange Mass Spectrometry to Examine Protein-Membrane Interactions

Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS experiments measure protein conformational dynamics in their native state, based on the rate of exchange of amide hydrogens with solvent. This review discusses the use of HDX-MS as a tool to identify the interfaces of proteins with membranes and membrane-associated proteins, as well as define conformational changes elicited by membrane recruitment. Specific examples will focus on the use of HDX-MS to examine how large macromolecular protein complexes are recruited and activated on membranes, and how both posttranslational modifications and cancer-linked oncogenic mutations affect these processes.

Spliceosome assembly in the absence of stable U4/U6 RNA pairing

The cycle of spliceosome assembly, intron excision, and spliceosome disassembly involves large-scale structural rearrangements of U6 snRNA that are functionally important. U6 enters the splicing pathway bound to the Prp24 protein, which chaperones annealing of U6 to U4 RNA to form a U4/U6 di-snRNP. During catalytic activation of the assembled spliceosome, U4 snRNP is released and U6 is paired to U2 snRNA. Here we show that point mutations in U4 and U6 that decrease U4/U6 base-pairing in vivo are lethal in combination. However, this synthetic phenotype is rescued by a mutation in U6 that alters a U6-Prp24 contact and stabilizes U2/U6. Remarkably, the resulting viable triple mutant strain lacks detectable U4/U6 base-pairing and U4/U6 di-snRNP. Instead, this strain accumulates free U4 snRNP, protein-free U6 RNA, and a novel complex containing U2/U6 di-snRNP. Further mutational analysis indicates that disruption of the U6-Prp24 interaction rather than stabilization of U2/U6 renders stable U4/U6 di-snRNP assembly nonessential. We propose that an essential function of U4/U6 pairing is to displace Prp24 from U6 RNA, and thus a destabilized U6-Prp24 complex renders stable U4/U6 pairing nonessential.

Nucleic acid structure characterization by small angle X-ray scattering (SAXS)

Small angle X-ray scattering (SAXS) is a powerful method for investigating macromolecular structure in solution. SAXS data provide information about the size and shape of a molecule with a resolution of ∼2 to 3 nm. SAXS is particularly useful for the investigation of nucleic acids, which scatter X-rays strongly due to the electron-rich phosphate backbone. Therefore, SAXS has become an increasingly popular method for modeling nucleic acid structures, an endeavor made tractable by the highly regular helical nature of nucleic acid secondary structures. Recently, SAXS was used in combination with NMR to filter and refine all-atom models of a U2/U6 small nuclear RNA complex. In this unit, general protocols for sample preparation, data acquisition, and data analysis and processing are given. Additionally, examples of correctly and incorrectly processed SAXS data and expected results are provided.

Structure of the yeast U2/U6 snRNA complex

The U2/U6 snRNA complex is a conserved and essential component of the active spliceosome that interacts with the pre-mRNA substrate and essential protein splicing factors to promote splicing catalysis. Here we have elucidated the solution structure of a 111-nucleotide U2/U6 complex using an approach that integrates SAXS, NMR, and molecular modeling. The U2/U6 structure contains a three-helix junction that forms an extended "Y" shape. The U6 internal stem-loop (ISL) forms a continuous stack with U2/U6 Helices Ib, Ia, and III. The coaxial stacking of Helix Ib on the U6 ISL is a configuration that is similar to the Domain V structure in group II introns. Interestingly, essential features of the complex--including the U80 metal binding site, AGC triad, and pre-mRNA recognition sites--localize to one face of the molecule. This observation suggests that the U2/U6 structure is well-suited for orienting substrate and cofactors during splicing catalysis.

The effect of race and sex on physicians' recommendations for cardiac catheterization

BACKGROUND

Epidemiologic studies have reported differences in the use of cardiovascular procedures according to the race and sex of the patient. Whether the differences stem from differences in the recommendations of physicians remains uncertain.

METHODS

We developed a computerized survey instrument to assess physicians' recommendations for managing chest pain. Actors portrayed patients with particular characteristics in scripted interviews about their symptoms. A total of 720 physicians at two national meetings of organizations of primary care physicians participated in the survey. Each physician viewed a recorded interview and was given other data about a hypothetical patient. He or she then made recommendations about that patient's care. We used multivariate logistic-regression analysis to assess the effects of the race and sex of the patients on treatment recommendations, while controlling for the physicians' assessment of the probability of coronary artery disease as well as for the age of the patient, the level of coronary risk, the type of chest pain, and the results of an exercise stress test.

RESULTS

The physicians' mean (+/-SD) estimates of the probability of coronary artery disease were lower for women (probability, 64.1+/-19.3 percent, vs. 69.2+/-18.2 percent for men; P<0.001), younger patients (63.8+/-19.5 percent for patients who were 55 years old, vs. 69.5+/-17.9 percent for patients who were 70 years old; P<0.001), and patients with nonanginal pain (58.3+/-19.0 percent, vs. 64.4+/-18.3 percent for patients with possible angina and 77.1+/-14.0 percent for those with definite angina; P=0.001). Logistic-regression analysis indicated that women (odds ratio, 0.60; 95 percent confidence interval, 0.4 to 0.9; P=0.02) and blacks (odds ratio, 0.60; 95 percent confidence interval, 0.4 to 0.9; P=0.02) were less likely to be referred for cardiac catheterization than men and whites, respectively. Analysis of race-sex interactions showed that black women were significantly less likely to be referred for catheterization than white men (odds ratio, 0.4; 95 percent confidence interval, 0.2 to 0.7; P=0.004).

CONCLUSIONS

Our findings suggest that the race and sex of a patient independently influence how physicians manage chest pain.

Dental research. What priority in the academic environment?

The priority given to dental research in academics is controversial. There exists the pressure for all academicians to pursue funding and publication of research as a major criterion for promotion. This is difficult for those clinical faculty not trained or unable to perform valid investigations. Training of new researchers is important if only to ensure that quality research will be performed in the future. Industry can assist as a good source of funding and increased opportunity in dental research.

Systemic lupus erythematosus circulating anticoagulant: report of a case

A patient without lupus erythematosus in whom a routine presurgical work-up resulted in discovery of the SLE circulating antibody is described. The diagnosis and treatment are discussed.

Systems analysis of schools of allied health using Leavitt's Organizational Model: a meta-analysis

Schools of allied health are relative newcomers to the formal academic setting. Consequently, these new academic units are particularly vulnerable to external threats to survival as they struggle to achieve acceptance by faculty and administrators in the traditional disciplines. This paper describes an application of Leavitt's Organizational Model for systems analysis of schools of allied health. A meta-analysis of studies reported in the Journal of Allied Health was conducted to provide administrative insight for the model's dimensions of task, structure, technology, and people. The model is helpful in organizing information and predicting effects of intervention strategies when any single dimension is changed. By viewing schools of allied health from a holistic perspective, deans and chair persons can anticipate the effect of change on variables (dimensions) other than those being manipulated and weight intervention strategies before their adoption.

The comparison of 8-hydroxyquinoline, tropolone, and acetylacetone as mediators in the labelling of polymorphonuclear leucocytes with indium-111: a functional study

Tropolone forms a lipophilic complex with indium-111 which is capable of mediating the labelling of polymorphonuclear leucocytes (PMNs) by this isotope; labelling efficiencies are comparable with the best achieved using 8-hydroxyquinoline and acetylacetone. However, in terms of PMN chemotaxis and phagocytosis, tropolone is significantly less toxic than either of te other ligands. 8-Hydroxyquinoline was found to reduce PMN chemotaxis and phagocytosis to approximately 70% of the control values at a concentration of 20 micro M. Tropolone may prove a superior labelling reagent.

Inflight measurement of pilot workload: a panel discussion

A group of U.S. scientists engaged in inflight measurements of pilot workload discussed the problems and aspects of workload; the techniques used for inflight measurements; the various workload models, such as design-oriented, operational, psychological, and physiological concepts; different experimental approaches; and experiences, results and further plans, during the 48th Annual Scientific Meeting of the Aerospace Medical Association in Las Vegas, Nv, on May 10, 1977. The contributions by the chairman and the five panel members are summarized.

Scattering by two-component random distributions of spheres

Theory and prototype (at wavelength lambda = 5 mm) partial coherence scattering data for optical applications in diagnostic measurements on two component suspensions or gases are presented. Results are given for equal volume mixtures of two sizes of moving randomly distributed large spheres for all realizable values of the fractional volume w (the fraction of the slab region container filled by scattering material). The relative index of refraction of the spheres was about 1.017, and their diameters were 6.52lambda and 3.33lambda (so that we used about eight times as many small spheres as large ones for each value of w). The spheres were of lightweight Styrofoam, and their motion arose from turbulent air streams (flowing through grids that form the top and bottom of a Styrofoam container), and the data were obtained in real time by processing the instantaneous phase quadrature components of the scattered field with an electronic analog computer. We give results for the forward scattered coherent phase, for the coherent, incoherent, and total intensities, and for the covariant magnitude and phase which (together with the incoherent intensity) provide the variances and covariance of the instantaneous phase quadrature components. We also consider certain reduced data records (from which the major effects of scatterer size and material have been eliminated) to indicate the dependence of the scattering on the fractional volume and to facilitate comparison with earlier data for distributions of identical spheres.