Regularized sequence-context mutational trees capture variation in mutation rates across the human genome.

Germline mutation is the mechanism by which genetic variation in a population is created. Inferences derived from mutation rate models are fundamental to many population genetics methods. Previous models have demonstrated that nucleotides flanking polymorphic sites-the local sequence context-explain variation in the probability that a site is polymorphic. However, limitations to these models exist as the size of the local sequence context window expands. These include a lack of robustness to data sparsity at typical sample sizes, lack of regularization to generate parsimonious models and lack of quantified uncertainty in estimated rates to facilitate comparison between models. To address these limitations, we developed Baymer, a regularized Bayesian hierarchical tree model that captures the heterogeneous effect of sequence contexts on polymorphism probabilities. Baymer implements an adaptive Metropolis-within-Gibbs Markov Chain Monte Carlo sampling scheme to estimate the posterior distributions of sequence-context based probabilities that a site is polymorphic. We show that Baymer accurately infers polymorphism probabilities and well-calibrated posterior distributions, robustly handles data sparsity, appropriately regularizes to return parsimonious models, and scales computationally at least up to 9-mer context windows. We demonstrate application of Baymer in three ways-first, identifying differences in polymorphism probabilities between continental populations in the 1000 Genomes Phase 3 dataset, second, in a sparse data setting to examine the use of polymorphism models as a proxy for de novo mutation probabilities as a function of variant age, sequence context window size, and demographic history, and third, comparing model concordance between different great ape species. We find a shared context-dependent mutation rate architecture underlying our models, enabling a transfer-learning inspired strategy for modeling germline mutations. In summary, Baymer is an accurate polymorphism probability estimation algorithm that automatically adapts to data sparsity at different sequence context levels, thereby making efficient use of the available data.

Mechanism of Hsp70 specialized interactions in protein translocation and the unfolded protein response.

Hsp70 chaperones interact with substrate proteins in a coordinated fashion that is regulated by nucleotides and enhanced by assisting cochaperones. There are numerous homologues and isoforms of Hsp70 that participate in a wide variety of cellular functions. This diversity can facilitate adaption or specialization based on particular biological activity and location within the cell. In this review, we highlight two specialized binding partner proteins, Tim44 and IRE1, that interact with Hsp70 at the membrane in order to serve their respective roles in protein translocation and unfolded protein response signalling. Recent mechanistic data suggest analogy in the way the two Hsp70 homologues (BiP and mtHsp70) can bind and release from IRE1 and Tim44 upon substrate engagement. These shared mechanistic features may underlie how Hsp70 interacts with specialized binding partners and may extend our understanding of the mechanistic repertoire that Hsp70 chaperones possess.

UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor.

BiP is a major endoplasmic reticulum (ER) chaperone and is suggested to act as primary sensor in the activation of the unfolded protein response (UPR). How BiP operates as a molecular chaperone and as an ER stress sensor is unknown. Here, by reconstituting components of human UPR, ER stress and BiP chaperone systems, we discover that the interaction of BiP with the luminal domains of UPR proteins IRE1 and PERK switch BiP from its chaperone cycle into an ER stress sensor cycle by preventing the binding of its co-chaperones, with loss of ATPase stimulation. Furthermore, misfolded protein-dependent dissociation of BiP from IRE1 is primed by ATP but not ADP. Our data elucidate a previously unidentified mechanistic cycle of BiP function that explains its ability to act as an Hsp70 chaperone and ER stress sensor.

Structure and Molecular Mechanism of ER Stress Signaling by the Unfolded Protein Response Signal Activator IRE1.

The endoplasmic reticulum (ER) is an important site for protein folding and maturation in eukaryotes. The cellular requirement to synthesize proteins within the ER is matched by its folding capacity. However, the physiological demands or aberrations in folding may result in an imbalance which can lead to the accumulation of misfolded protein, also known as "ER stress." The unfolded protein response (UPR) is a cell-signaling system that readjusts ER folding capacity to restore protein homeostasis. The key UPR signal activator, IRE1, responds to stress by propagating the UPR signal from the ER to the cytosol. Here, we discuss the structural and molecular basis of IRE1 stress signaling, with particular focus on novel mechanistic advances. We draw a comparison between the recently proposed allosteric model for UPR induction and the role of Hsp70 during polypeptide import to the mitochondrial matrix.

On-Demand Final State Control of a Surface-Bound Bistable Single Molecule Switch.

Modern electronic devices perform their defined action because of the complete reliability of their individual active components (transistors, switches, diodes, and so forth). For instance, to encode basic computer units (bits) an electrical switch can be used. The reliability of the switch ensures that the desired outcome (the component's final state, 0 or 1) can be selected with certainty. No practical data storage device would otherwise exist. This reliability criterion will necessarily need to hold true for future molecular electronics to have the opportunity to emerge as a viable miniaturization alternative to our current silicon-based technology. Molecular electronics target the use of single-molecules to perform the actions of individual electronic components. On-demand final state control over a bistable unimolecular component has therefore been one of the main challenges in the past decade (1-5) but has yet to be achieved. In this Letter, we demonstrate how control of the final state of a surface-supported bistable single molecule switch can be realized. On the basis of the observations and deductions presented here, we further suggest an alternative strategy to achieve final state control in unimolecular bistable switches.

In vitro FRET analysis of IRE1 and BiP association and dissociation upon endoplasmic reticulum stress.

The unfolded protein response (UPR) is a key signaling system that regulates protein homeostasis within the endoplasmic reticulum (ER). The primary step in UPR activation is the detection of misfolded proteins, the mechanism of which is unclear. We have previously suggested an allosteric mechanism for UPR induction (Carrara et al., 2015) based on qualitative pull-down assays. Here, we develop an in vitro Förster resonance energy transfer (FRET) UPR induction assay that quantifies IRE1 luminal domain and BiP association and dissociation upon addition of misfolded proteins. Using this technique, we reassess our previous observations and extend mechanistic insight to cover other general ER misfolded protein substrates and their folded native state. Moreover, we evaluate the key BiP substrate-binding domain mutant V461F. The new experimental approach significantly enhances the evidence suggesting an allosteric model for UPR induction upon ER stress.

Abnormal glycosylation in Joubert syndrome type 10.

BACKGROUND: The discovery of disease pathogenesis requires systematic agnostic screening of multiple homeostatic processes that may become deregulated. We illustrate this principle in the evaluation and diagnosis of a 5-year-old boy with Joubert syndrome type 10 (JBTS10). He carried the OFD1 mutation p.Gln886Lysfs*2 (NM_003611.2: c.2656del) and manifested features of Joubert syndrome. METHODS: We integrated exome sequencing, MALDI-TOF mass spectrometry analyses of plasma and cultured dermal fibroblasts glycomes, and full clinical evaluation of the proband. Analyses of cilia formation and lectin staining were performed by immunofluorescence. Measurement of cellular nucleotide sugar levels was performed with high-performance anion-exchange chromatography with pulsed amperometric detection. Statistical analyses utilized the Student's and Fisher's exact t tests. RESULTS: Glycome analyses of plasma and cultured dermal fibroblasts identified abnormal N- and O-linked glycosylation profiles. These findings replicated in two unrelated males with OFD1 mutations. Cultured fibroblasts from affected individuals had a defect in ciliogenesis. The proband's fibroblasts also had an abnormally elevated nuclear sialylation signature and increased total cellular levels of CMP-sialic acid. Ciliogenesis and each glycosylation anomaly were rescued by expression of wild-type OFD1. CONCLUSIONS: The rescue of ciliogenesis and glycosylation upon reintroduction of WT OFD1 suggests that both contribute to the pathogenesis of JBTS10.

Explorations to improve the completeness of exome sequencing.

BACKGROUND: Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis. Such false negatives reflect limitations in experimental design, technical performance, and data analysis. RESULTS: We present examples from our datasets to quantify the analytical performance associated with current practices, and explore strategies to improve the completeness of data analysis. In particular, we focus on patient ascertainment, exome capture, inclusion of intronic variants, and evaluation of medium-sized structural variants. CONCLUSIONS: The strategies we present may recover previously-missed, disease causing variants in second-pass exome analysis. Understanding the limitations of the current clinical exome search space provides a rational basis to improve methods for disease variant detection using genome-scale sequencing techniques.

Two-step solid-state synthesis of PEPPSI-type compounds.

The two-step mechanochemical preparation of carbene-pyridine complexes of palladium and platinum is reported. The organometallic products, which represent a class of commercially available catalysts, are rapidly formed in excellent yield proving solvent-free synthesis to be a viable synthetic alternative even in the case of NHC-containing compounds.

Isolation of maltol glucoside from the floral nectar of New Zealand manuka (Leptospermum scoparium).

Maltol glucoside (3-(ß-D-glucopyranosyloxy)-2-methyl-4H-pyran-4-one), 1, was isolated from a preparation of the floral nectar from the New Zealand manuka tree (Leptospermum scoparium). 1 eluted just after dihydroxyacetone in HPLC of underivatized nectar and showed a UV absorbance maximum of 258 nm. The structure of 1 was confirmed by NMR and high resolution mass spectrometry.

New class of metal bound molecular switches involving H-tautomerism.

A potential end-point in the miniaturization of electronic devices lies in the field of molecular electronics, where molecules perform the function of single components. To date, hydrogen tautomerism in unimolecular switches has been restricted to the central macrocycle of porphyrin-type molecules. The present work reveals how H-tautomerism is the mechanism for switching in substituted quinone derivatives, a novel class of molecules with a different chemical structure. We hence reveal that the previous restrictions applying to tautomeric molecular switches bound to a surface are not valid in general. The activation energy of switching in a prototypical quinone derivative is determined using inelastic electron tunneling. Through computational modeling, we show that the mechanism underlying this process is tautomerization of protons belonging to two amino groups. This switching property is retained upon functionalization by the addition of side groups, meaning that the switch can be chemically modified to fit specific applications.

A polycyclic borazine radical cation: [1,2-B2{1,2-(MeN)2C6H4}2]˙(+).

The radical cation [1,2-B2{1,2-(MeN)2C6H4}2]˙(+) has been synthesised and its structure and bonding have been probed using a combination of X-ray crystallography, EPR spectroscopy and DFT calculations which show that it represents a new type of radical centred primarily on two N-heterocyclic units joined by a B2 linker but with only a minor contribution from boron-based orbitals.

Iron(I) in Negishi cross-coupling reactions.

Herein we demonstrate both the importance of Fe(I) in Negishi cross-coupling reactions with arylzinc reagents and the isolation of catalytically competent Fe(I) intermediates. These complexes, [FeX(dpbz)(2)] [X = 4-tolyl (7), Cl (8a), Br (8b); dpbz = 1,2-bis(diphenylphosphino)benzene], were characterized by crystallography and tested for activity in representative reactions. The complexes are low-spin with no significant spin density on the ligands. While complex 8b shows performance consistent with an on-cycle intermediate, it seems that 7 is an off-cycle species.

Mechanochemistry: opportunities for new and cleaner synthesis.

The aim of this critical review is to provide a broad but digestible overview of mechanochemical synthesis, i.e. reactions conducted by grinding solid reactants together with no or minimal solvent. Although mechanochemistry has historically been a sideline approach to synthesis it may soon move into the mainstream because it is increasingly apparent that it can be practical, and even advantageous, and because of the opportunities it provides for developing more sustainable methods. Concentrating on recent advances, this article covers industrial aspects, inorganic materials, organic synthesis, cocrystallisation, pharmaceutical aspects, metal complexes (including metal-organic frameworks), supramolecular aspects and characterization methods. The historical development, mechanistic aspects, limitations and opportunities are also discussed (314 references).

Cooperative spin transition in the two-dimensional coordination polymer [Fe(4,4'-bipyridine)2(NCX)2]·4CHCl3 (X = S, Se).

Two new isostructural two-dimensional (2D) coordination polymers exhibiting spin crossover (SCO) behavior of formulation [Fe(4,4'-bipy)(2)(NCX)(2)]·4CHCl(3) (4,4'-bipy = 4,4'-bipyridine; X = S [1·4CHCl(3)], Se [2·4CHCl(3)]) have been synthesized and characterized, and both undergo cooperative spin transitions (ST). For 1·4CHCl(3) the ST takes place in two steps with critical temperatures of T(c1)(down) = 143.1 K, T(c2)(down) = 91.2 K, T(c1)(up) = 150.7 K, and T(c2)(up) = 112.2 K. 2·4CHCl(3) displays half ST characterized by T(c)(down) = 161.7 K and T(c)(up) = 168.3 K. The average enthalpy and entropy variations and cooperativity parameters associated with the ST have been estimated to be ΔH(1)(av) = 5.18 kJ mol(-1), ΔS(1)(av) = 35 J K(-1) mol(-1), and Γ(1) = 2.8 kJ mol(-1) and ΔH(2)(av) = 3.55 kJ mol(-1), ΔS(2)(av) = 35 J K(-1) mol(-1), and Γ(2) = 2.6 kJ mol(-1) for 1·4CHCl(3), and ΔH(av) = 6.25 kJ mol(-1), ΔS(av) = 38.1 J K(-1) mol(-1), and Γ = 3.2 kJ mol(-1) for 2·4CHCl(3). At T > [T(c1) (1·4CHCl(3)); T(c) (2·4CHCl(3))], both compounds are in the space group P2/c while at T < [T(c1) (1·4CHCl(3)); T(c) (2·4CHCl(3))] they change to the C2/c space group and display an ordered checkerboard-like arrangement of iron(II) sites where the high- and low-spin states coexist at 50%.

Syntheses of Group 4 ansa-trovacene complexes and conversion of [1]silatrovacenophanes into paramagnetic metallopolymers by ring-opening polymerization.

An improved protocol for the selective dilithiation of [V(η(5)-C(5)H(5))(η(7)-C(7)H(7))] has been developed, which afforded [V(η(5)-C(5)H(4)Li)(η(7)-C(7)H(6)Li)]·PMDTA (5; PMDTA=N,N,N',N'',N''-pentamethyldiethylenetriamine) in almost quantitative yield (98%). In the solid state, the species features a dimeric structure with two terminal and two bridging lithium atoms, with the latter connecting both sandwich subunits. Reaction with suitable Group 4 dihalide compounds enabled the isolation of highly strained silicon- and germanium-bridged [1]trovacenophanes 6 and 7. Similarly, reaction of 5 with Cl(2)Sn(2)tBu(4) afforded the rather unstrained complex [V(η(5)-C(5)H(4))(η(7)-C(7)H(6))Sn(2)tBu(4)] (8), which together with 7 represent the first trovacenophanes to incorporate heavier analogues of silicon in the ansa-bridge. Ring-opening polymerization reactions of [V(η(5)-C(5)H(4))(η(7)-C(7)H(6))SiRR'] (2a: R=R'=Me; 6: R=Me, R'=iPr) were performed by heating in a solution of toluene in the presence of the Karstedt catalyst, which resulted in the formation of the corresponding soluble poly(trovacenylsilanes) in yields of 41 and 33%, respectively. As estimated by gel permeation chromatography (GPC), the macromolecules possess molecular weights of M(n)=10,010 and 5580 g mol(-1) with polydispersity indices of 2.31 and 1.64 for 9 and 10, respectively. ESR spectroscopic studies on 9 and 10 revealed only a single broad resonance in each case without any identifiable (51)V hyperfine coupling.

Coordination chemistry in the solid state: reactivity of manganese and cadmium chlorides with imidazole and pyrazole and their hydrochlorides.

Crystalline coordination compounds [MnCl(2)(Hpz)(2)] 3, [CdCl(2)(Hpz)(2)] 5, [MnCl(2)(Him)(2)] 9, and [CdCl(2)(Him)(2)] 13 (Him = imidazole; Hpz = pyrazole) can be synthesized in solid state reactions by grinding together the appropriate metal chloride and 2 equiv of the neutral ligand. Similarly, grinding together the metal chlorides with the ligand hydrochloride salts produces the halometallate salts [H(2)pz][MnCl(3)(OH(2))] 1, [H(2)pz][CdCl(4)] 4, [H(2)im](6)[MnCl(6)][MnCl(4)] 8, and [H(2)im](6)[CdCl(6)][CdCl(4)] 11. In contrast, reacting the metal chloride salt with the ligand in concentrated HCl solution yields a second set of salts [H(2)pz][MnCl(3)] 2, [H(2)im][MnCl(3)(OH(2))(2)] 7, and [H(2)im][CdCl(3)(OH(2))]·H(2)O 12. Compound 5 can be partly dehydrochlorinated by grinding with KOH to form an impure sample of the pyrazolate compound [Cd(pz)(2)] 6, while recrystallizing 9 from ethanol yielded crystals of solvated [Mn(4)Cl(8)(Him)(8)] 10. The crystal structure determinations of 1, 2, 4, 11, and 12 are reported.

Crystal engineering of lattice metrics of perhalometallate salts and MOFs.

The synthesis of the salt 3 and metallo-organic framework (MOF) [{(4,4(')-bipy)CoBr(2)}(n)] 4 by a range of solid state (mechanochemical and thermochemical) and solution methods is reported; they are isostructural with their respective chloride analogues 1 and 2. 3 and 4 can be interconverted by means of HBr elimination and absorption. Single phases of controlled composition and general formula [4,4(')-H(2)bipy][CoBr(4-x)Cl(x)] 5(x) may be prepared from 2 and 4 by solid--gas reactions involving HBr or HCl respectively. Crystalline single phase samples of 5(x) and [{(4,4(')-bipy)CoBr(2-x)Cl(x)}(n)] 6(x) were prepared by solid-state mechanochemical routes, allowing fine control over the composition and unit cell volume of the product. Collectively these methods enable continuous variation of the unit cell dimensions of the salts [4,4(')-H(2)bipy][CoBr(4-x)Cl(x)] (5(x)) and the MOFs [{(4,4(')-bipy)CoBr(2-x)Cl(x)}(n)] (6(x)) by varying the bromide to chloride ratio and establish a means of controlling MOF composition and the lattice metrics, and so the physical and chemical properties that derive from it.

Synthesis and characterisation of the persistent radical [BCl2(bipy)]*.

The persistent radical, [BCl(2)(bipy)](*) (bipy = 2,2'-bipyridyl), has been prepared and characterised by X-ray crystallography, ESR and DFT calculations. The structure is compared with that of the cation, [BCl(2)(bipy)](+).