De novo construction of polyploid linkage maps using discrete graphical models

Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. We propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a nonparanormal skeptic approach. Linkage groups (LGs), typically chromosomes, and the order of markers in each LG are determined by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors and are incomplete. We apply the proposed method to two genotype datasets: barley and potato from diploid and polypoid populations, respectively. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We have implemented the method in the R package netgwas.Comment: 25 pages, 7 figure

netgwas: An R Package for Network-Based Genome-Wide Association Studies

Graphical models are powerful tools for modeling and making statistical inferences regarding complex associations among variables in multivariate data. In this paper we introduce the R package netgwas, which is designed based on undirected graphical models to accomplish three important and interrelated goals in genetics: constructing linkage map, reconstructing linkage disequilibrium (LD) networks from multi-loci genotype data, and detecting high-dimensional genotype-phenotype networks. The netgwas package deals with species with any chromosome copy number in a unified way, unlike other software. It implements recent improvements in both linkage map construction (Behrouzi and Wit, 2018), and reconstructing conditional independence network for non-Gaussian continuous data, discrete data, and mixed discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely occur in genetics and genomics such as genotype data, and genotype-phenotype data. We demonstrate the value of our package functionality by applying it to various multivariate example datasets taken from the literature. We show, in particular, that our package allows a more realistic analysis of data, as it adjusts for the effect of all other variables while performing pairwise associations. This feature controls for spurious associations between variables that can arise from classical multiple testing approach. This paper includes a brief overview of the statistical methods which have been implemented in the package. The main body of the paper explains how to use the package. The package uses a parallelization strategy on multi-core processors to speed-up computations for large datasets. In addition, it contains several functions for simulation and visualization. The netgwas package is freely available at https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot be longer than 1,920 characters", the abstract appearing here is slightly shorter than that in the PDF fil

Carbonate-Templated Self-Assembly of an Alkylthiolate-Bridged Cadmium Macrocycle

In the presence of Cd(ClO4)2 and a base, a new mixed N,S-donor alkylthiolate ligand supported both carbonate formation from atmospheric CO2 and the self-assembly of a novel bicapped puckered (CdS)6 molecular wheel. The remarkable stability of the complex was demonstrated by slow intermolecular ligand exchange on the 2J(HH) and J(111/113Cd1H) time scales at elevated temperature. Both CO2 and the base were required to convert amorphous “CdLClO4” precipitated in the absence of air to the carbonate complex. The complex shares structural features with the ζ-carbonic anhydrase class associating cadmium(II) with the biogeochemical cycling of carbon and is the first structurally characterized carbonate complex of any metal involving an alkylthiolate ligand

A Novel T-Cell Engaging Bi-specific Antibody Targeting the Leukemia Antigen PR1/HLA-A2

Despite substantial advances in the treatment of acute myeloid leukemia (AML), only 30% of patients survive more than 5 years. Therefore, new therapeutics are much needed. Here, we present a novel therapeutic strategy targeting PR1, an HLA-A2 restricted myeloid leukemia antigen. Previously, we have developed and characterized a novel T-cell receptor-like monoclonal antibody (8F4) that targets PR1/HLA-A2 and eliminates AML xenografts by antibody-dependent cellular cytotoxicity (ADCC). To improve the potency of 8F4, we adopted a strategy to link T-cell cytotoxicity with a bi-specific T-cell-engaging antibody that binds PR1/HLA-A2 on leukemia and CD3 on neighboring T-cells. The 8F4 bi-specific antibody maintained high affinity and specific binding to PR1/HLA-A2 comparable to parent 8F4 antibody, shown by flow cytometry and Bio-Layer Interferometry. In addition, 8F4 bi-specific antibody activated donor T-cells in the presence of HLA-A2+ primary AML blasts and cell lines in a dose dependent manner. Importantly, activated T-cells lysed HLA-A2+ primary AML blasts and cell lines after addition of 8F4 bi-specific antibody. In conclusion, our studies demonstrate the therapeutic potential of a novel bi-specific antibody targeting the PR1/HLA-A2 leukemia-associated antigen, justifying further clinical development of this strategy

New discrete and polymeric supramolecular architectures derived from dinuclear Co(II), Ni(II) and Cu(II) complexes of aryl-linked bis-beta-diketonato ligands and nitrogen bases: synthetic, structural and high pressure studies

New examples of nitrogen base adducts of dinuclear Co(II), Ni(II) and Cu(II) complexes of the doubly deprotonated forms of 1,3-aryl linked bis-β-diketones of type [RC([double bond, length as m-dash]O)CH2C([double bond, length as m-dash]O)C6H4C([double bond, length as m-dash]O)CH2C([double bond, length as m-dash]O)R] (L1H2) incorporating the mono- and difunctional amine bases pyridine (Py), 4-ethylpyridine (EtPy), piperidine (pipi), 1,4-piperazine (pip), N-methylmorpholine (mmorph), 1,4-dimethylpiperazine (dmpip) and N,N,N′,N′-tetramethylethylenediamine (tmen) have been synthesised by reaction of the previously reported [Cu2(L1)2]·2.5THF (R = Me), [Cu2(L1)2(THF)2] (R = t-Bu), [Ni2(L1)2(Py)4] (R = t-Bu) and [Co2(L1)2(Py)4] (R = t-Bu) complexes with individual bases of the above type. Comparative X-ray structural studies involving all ten base adduct derivatives have been obtained and reveal a range of interesting discrete and polymeric molecular architectures. The respective products have the following stoichiometries: [Cu2(L1)2(Py)2]·Py (R = Me), [Cu2(L1)2(EtPy)2]·2EtPy (R = t-Bu), [Cu2(L1)2(pipi)2]·2pipi (R = t-Bu), [Cu2(L1)2(mmorph)2] (R = t-Bu), [Cu2(L1)2(tmen)2] (R = t-Bu) and {[Cu2(L1)2(pip)]·pip·2THF}n, [Co2(L1)2(tmen)2] (R = t-Bu), [Ni2(L1)2(Py)4]·dmpip (R = t-Bu), [Ni2(L1)2(pipi)4]·pipi (R = t-Bu) and [Ni2(L1)2(tmen)2] (R = t-Bu). The effect of pressure on the X-ray structure of [Cu2(L1)2(mmorph)2] has been investigated. An increase in pressure from ambient to 9.1 kbar resulted in modest changes to the unit cell parameters as well as a corresponding decrease of 6.7 percent in the unit cell volume. While a small ‘shearing’ motion occurs between adjacent molecular units throughout the lattice, no existing bonds are broken or new bonds formed

Syntheses and X-ray crystal structures of [Zn(cyclen)-im-Zn(cyclen)](ClO4)(3) and [Ni(cyclen)(imH)(ClO4)](ClO4) (cyclen=1,4,7,10-tetraazacyclododecane, im=imidazolate)

[[abstract]]The imidazolate-bridged binuclear zinc(II) macrocyclic complex, [Zn(cyclen)-im-Zn(cyclen)](ClO4)(3) (1) and the free imidazole coordinated mononuclear nickel(II) complex, [Ni(cyclen)(imH)(ClO4)](ClO4) (2) (cyclen=1,4,7,10-tetraazacyclododecane, im = imidazolate) have been synthesized. Complexes 1 and 2 have been characterized by single crystal structural analyses. In complex 1 both zinc(II) ions are five-coordinated with a distorted square pyramidal geometry composed of four nitrogen atoms from cyclen and one nitrogen atom from the bridging imidazolate ion with N-5 chromophore. Complex 2 is mononuclear nickel(II) having six-coordination with distorted octahedral geometry consisting of four nitrogen atoms from cyclen, one nitrogen atom from the imidazole molecule and one oxygen from one of the perchlorate ions to give a N5O chromophore.[[fileno]]2010337010177[[department]]化學

Metallohexacycles containing 4′-aryl-4,2′:6′,4′′-terpyridines: conformational preferences and fullerene capture

4′-(4-Biphenylyl)-4,2′:6′,4′′-terpyridine (1) reacts with ZnCl2 or ZnBr2 to produce discrete metallohexacycles instead of the expected one-dimensional coordination polymers. Structural determination of [{ZnCl2(1)}6] and [{ZnBr2(1)}6] reveals that the metallomacrocycles adopt a conformation in which the biphenyl domains are in an alternating up/down arrangement (conformer I). The hexamers pack into tubes; within each tube, biphenyl domains of every second hexamer are interdigitated, and these assemblies then interlock to produce a rigid architecture supported by pyridine–phenyl face-to-face contacts. π-Stacking between 4,2′:6′,4′′-tpy domains operates between adjacent tubes. Reaction of ZnCl2 or ZnBr2 with 4′-(2′,3′,4′,5′,6′-pentafluorobiphenyl-4-yl)-4,2′:6′,4′′-terpyridine (2) leads to [{ZnCl2(2)}6] and [{ZnBr2(2)}6], each crystallizing in two conformations; the centrosymmetric chair-conformer (II) is dominant with respect to the tub-like conformer I. Both conformers pack into tube assemblies, but that consisting of conformer II is less rigid than that of I. Reaction of 4′-(4-(naphthalen-1-yl)phenyl)-4,2′:6′,4′′-terpyridine (3) with ZnCl2 or ZnBr2 leads to [{ZnX2(2)}6] (X = Cl, Br) in conformer I; disordering of the naphthyl substituents is problematic. Assembly of the metallohexacycle in the presence of C60 results in the formation of the host–guest complex [2{ZnCl2(3)}6·C60]·6MeOH·16H2O. The [{ZnCl2(3)}6] units assemble into a tube-like array that mimics that observed in the parent host. In the host–guest complex, each crystallographically-ordered C60 is trapped between six ordered naphthyl units, three from one hexamer and three from its interdigitated partner, and the C60–six-naphthyl unit sits centrally within a second [{ZnCl2(3)}6] macrocycle. In contrast to previously described tube-like host–guest assemblies featuring fullerene entrapment, [2{ZnCl2(3)}6·C60] is unusual in having an ordered array of C60 molecules present in every other available cavity, despite the fact that sterically, the ‘empty’ cavity could, in principle, host a C60 guest

Clinical utility of the UCSD Performance-Based Skills Assessment-Brief (UPSA-B) in adults living with HIV: Associations with neuropsychological impairment and patient-reported everyday functioning difficulties.

ObjectiveRequiring only 10-15 minutes to complete, the UCSD Performance-Based Skills Assessment (UPSA-B) has high clinical utility as a brief measure of functional capacity. This study aimed to validate the UPSA-B in adults living with HIV/AIDS (HIV+), and identify whether the UPSA-B can be used as an indicator of functional dependence in this population.MethodOne hundred and three HIV+ adults and 91 HIV- adults completed a comprehensive neuropsychological and neuromedical battery, including a self-report measure of functional status (IADL Dependence vs. IADL Independence), an objective measure of functional capacity (UPSA-B), and a self-report measure of mood states including a subscale related to cognitive difficulties (Profile of Mood States [POMS]-Confusion/Bewilderment subscale).ResultsHIV+ participants had significantly lower UPSA-B scores than their HIV- counterparts (p = 0.02), although this fell to a trend (p = 0.08) when including covariates. Among the HIV+ group, higher UPSA-B scores were related to better neuropsychological ability, but unrelated to self-reported functional independence. Conversely, UPSA-B scores were unrelated to participant-reported cognitive difficulties on the POMS Confusion/Bewilderment subscale. An ROC curve was generated to determine the optimal UPSA-B value for discriminating between normal neuropsychological functioning versus neuropsychological impairment, with results indicating an optimal cutoff of 79. The UPSA-B identified HIV+ persons with cognitive impairment with 70.9% accuracy.ConclusionsThe UPSA-B was able to differentiate neuropsychological impairment from no impairment among HIV+ participants and holds promise as a clinical screening tool in this population. However, indicators of functional disability among adults living with HIV is still not well understood and is likely multifactorial in nature. These data highlight the complex interplay between objective functional capacity, neurocognitive ability, subjective cognitive symptoms, and functional dependence