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.

Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data.

Analyses of genetic variation typically assume that rare variants within a population are inherited from a single common ancestral event identity-by-descent (IBD). However, there are genetic and technical processes through which rare variants in population genetic data may deviate from this simple evolutionary model, including recurrent mutations, gene conversions and genotyping error. All these processes can decrease the expected length of shared background haplotype surrounding a rare variant if that variant was inherited from a single event descending from a common ancestor.

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.

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.

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.

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.

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.

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.

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.

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 mānuka (Leptospermum scoparium).

Maltol glucoside (3-(β-D-glucopyranosyloxy)-2-methyl-4H-pyran-4-one), 1, was isolated from a preparation of the floral nectar from the New Zealand mānuka 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.

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.

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.

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.

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.

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.

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.

Coordination chemistry in the solid state: synthesis and interconversion of pyrazolium salts, pyrazole complexes, and pyrazolate MOFs.

Solid pyrazole reacts with HCl gas to form pyrazolium chloride [H2pz]Cl, which reacts in the solid state, under grinding, with metal chlorides MCl2 (M = Co, Zn, Cu) to form the pyrazolium tetrachlorometallate salts [H2pz]2[MCl4] (M = Co 1, Zn 3, Cu 5). Salt 5 cannot be made in solution, and upon standing at room temperature spontaneously emits HCl to give the coordination compound [CuCl2(Hpz)2] (6). Compounds 1 and 3 do not exhibit this behaviour, but can be ground together with bases such as KOH or K2CO3 to effect the elimination of HCl and afford their respective [MCl2(Hpz)2] compounds (M = Co 2, Zn 4).

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)](+).

Homo- and heterodinuclear complexes of the tetrakis(pyrazolyl)borate ligand.

Monometallic complexes of the tetrakis(pyrazolyl)borate ligand [ML(2){B(pz)(4)}] {M = Rh, Ir; L(2) = eta-cod, eta-nbd, (CO)(2), (CO)(PPh(3))} have two free pyrazolyl rings which can be coordinated to a second ML(2) unit to give the dimeric compounds [L(2)M{mu-B(pz)(4)}ML(2)](+), and to a metal halide to give heterobimetallic species [L(2)M{mu-B(pz)(4)}M'Cl(2)]. (1)H NMR spectroscopy shows that [(eta-cod)Rh{mu-B(pz)(4)}Rh(eta-cod)](+) 1(+), [(eta-nbd)Rh{mu-B(pz)(4)}Rh(eta-nbd)](+) 2(+), [(eta-cod)Ir{mu-B(pz)(4)}Ir(eta-cod)](+) 3(+) and [(CO)(2)Rh{mu-B(pz)(4)}Rh(CO)(2)](+) 4(+) are fluxional at room temperature. Cooling a solution of [(eta-cod)Rh{mu-B(pz)(4)}Rh(eta-cod)](+) 1(+) to -90 degrees C slows the fluxional process, which involves inversion of the two B-(N-N)(2)-M six-membered rings.

Coordination chemistry of platinum and palladium in the solid-state: synthesis of imidazole and pyrazole complexes.

Solid-state reactions of palladium(II) and platinum(II) chloride complexes with imidazole (Him) and pyrazole (Hpz) or their hydrochloride salts are shown to produce metal complex salts and coordination compounds. Thus, K(2)[MCl(4)] or MCl(2) can be ground with imidazolium chloride ([H(2)im]Cl) to produce the salts [H(2)im](2)[MCl(4)] (M = Pd, 1; Pt, 5), which can then be dehydrochlorinated in the solid state to produce the coordination compounds trans-[PdCl(2)(Him)(2)] 3 or cis-[PtCl(2)(Him)(2)] 6. The complex cis-[PdCl(2)(Him)(2)] 2 is produced when Pd(OAc)(2) is ground with [H(2)im]Cl.

On the causes of potential inversion in 1,2,4,5-tetrakis(amino)benzenes.

Three 3,6-difluoro-1,2,4,5-tetrakis(amino)benzene compounds, bearing dimethylamino (1), piperidin-1-yl (3), or morpholin-1-yl (5) substituents, have been synthesized and subsequently defluorinated to give the corresponding 1,2,4,5-tetrakis(amino)benzene compounds 2, 4, and 6; the crystal structures of compounds 1, 4, and 6 have been obtained. Cyclic voltammetry shows that all six compounds will lose two electrons to form dications, and the use of suitable oxidizing agents has allowed isolation and crystallographic characterization of the dications 2(2+) and 6(2+) (as [PF(6)](2) salts) and 4(2+) (as a [I(5)][I(3)] salt). The separation DeltaE between the loss of the first electron and the second varies between compounds, from 0.