Whole-exome sequencing of T- B+ severe combined immunodeficiency in Egyptian infants, JAK3 predominance and novel variants.

Severe combined immunodeficiency (SCID) is fatal if not treated with immune reconstitution. In Egypt, T- B+ SCID accounts for 38·5% of SCID diagnoses. An accurate genetic diagnosis is essential for choosing appropriate treatment modalities and for offering genetic counseling to the patient's family. The objectives of this study were to describe the clinical, immunological and molecular characteristics of a cohort of twenty Egyptian patients with T- B+ SCID. The initial diagnosis (based on clinical features and flow cytometry) was followed by molecular investigation (whole-exome sequencing). All patients had the classic clinical picture for SCID, including failure to thrive (n = 20), oral candidiasis (n = 17), persistent diarrhea (n = 14), pneumonia (n = 13), napkin dermatitis (n = 10), skin rash (n = 7), otitis media (n = 3) and meningitis (n = 2). The onset of manifestations was at the age of 2·4 ± 1·6 months and diagnosis at the age of 6·7 ± ·5 months, giving a diagnostic delay of 4·3 months. JAK3 gene variants were most frequent (n = 12) with three novel variants identified, followed by IL2Rγ variants (n = 6) with two novel variants. IL7Rα and CD3ε variants were found once, with a novel variant each. T- B+ NK- SCID accounted for approximately 90% of the Egyptian patients with T- B+ SCID. Of these T- B+ NK- SCID cases, 60% were autosomal recessive syndromes caused by JAK3 mutations and 30% were X-linked syndromes. It might be useful to sequence the JAK3 gene (i.e. targeted Sanger sequencing) in all T- B+ SCID patients, especially after X-linked SCID has been ruled out. Hence, no more than 10% of T- B+ SCID patients might require next-generation for a molecular diagnosis.

Phenotypical heterogeneity in RAG-deficient patients from a highly consanguineous population.

Mutations affecting recombination activation genes RAG1 and RAG2 are associated with variable phenotypes, depending on the residual recombinase activity. The aim of this study is to describe a variety of clinical phenotypes in RAG-deficient patients from the highly consanguineous Egyptian population. Thirty-one patients with RAG mutations (from 28 families) were included from 2013 to 2017. On the basis of clinical, immunological and genetic data, patients were subdivided into three groups; classical T- B- severe combined immunodeficiency (SCID), Omenn syndrome (OS) and atypical SCID. Nineteen patients presented with typical T- B- SCID; among these, five patients carried a homozygous RAG2 mutation G35V and five others carried two homozygous RAG2 mutations (T215I and R229Q) that were detected together. Four novel mutations were reported in the T- B- SCID group; three in RAG1 (A565P, N591Pfs*14 and K621E) and one in RAG2 (F29S). Seven patients presented with OS and a novel RAG2 mutation (C419W) was documented in one patient. The atypical SCID group comprised five patients. Two had normal B cell counts; one had a previously undescribed RAG2 mutation (V327D). The other three patients presented with autoimmune cytopaenias and features of combined immunodeficiency and were diagnosed at a relatively late age and with a substantial diagnostic delay; one patient had a novel RAG1 mutation (C335R). PID disorders are frequent among Egyptian children because of the high consanguinity. RAG mutations stand behind several variable phenotypes, including classical SCID, OS, atypical SCID with autoimmunity and T- B+ CID.

Atomically resolved phase transition of fullerene cations solvated in helium droplets.

Helium has a unique phase diagram and below 25 bar it does not form a solid even at the lowest temperatures. Electrostriction leads to the formation of a solid layer of helium around charged impurities at much lower pressures in liquid and superfluid helium. These so-called 'Atkins snowballs' have been investigated for several simple ions. Here we form HenC60+ complexes with n exceeding 100 via electron ionization of helium nanodroplets doped with C60. Photofragmentation of these complexes is measured by merging a tunable narrow-bandwidth laser beam with the ions. A switch from red- to blueshift of the absorption frequency of HenC60+ on addition of He atoms at n=32 is associated with a phase transition in the attached helium layer from solid to partly liquid (melting of the Atkins snowball). Elaborate molecular dynamics simulations using a realistic force field and including quantum effects support this interpretation.

Adsorption of hydrogen on neutral and charged fullerene: experiment and theory.

Helium droplets are doped with fullerenes (either C60 or C70) and hydrogen (H2 or D2) and investigated by high-resolution mass spectrometry. In addition to pure helium and hydrogen cluster ions, hydrogen-fullerene complexes are observed upon electron ionization. The composition of the main ion series is (H2)(n)HC(m)(+) where m = 60 or 70. Another series of even-numbered ions, (H2)(n)C(m)(+), is slightly weaker in stark contrast to pure hydrogen cluster ions for which the even-numbered series (H2)(n)(+) is barely detectable. The ion series (H2)(n)HC(m)(+) and (H2)(n)C(m)(+) exhibit abrupt drops in ion abundance at n = 32 for C60 and 37 for C70, indicating formation of an energetically favorable commensurate phase, with each face of the fullerene ion being covered by one adsorbate molecule. However, the first solvation layer is not complete until a total of 49 H2 are adsorbed on C60(+); the corresponding value for C70(+) is 51. Surprisingly, these values do not exhibit a hydrogen-deuterium isotope effect even though the isotope effect for H2/D2 adsorbates on graphite exceeds 6%. We also observe doubly charged fullerene-deuterium clusters; they, too, exhibit abrupt drops in ion abundance at n = 32 and 37 for C60 and C70, respectively. The findings imply that the charge is localized on the fullerene, stabilizing the system against charge separation. Density functional calculations for C60-hydrogen complexes with up to five hydrogen atoms provide insight into the experimental findings and the structure of the ions. The binding energy of physisorbed H2 is 57 meV for H2C60(+) and (H2)2C60(+), and slightly above 70 meV for H2HC60(+) and (H2)2HC60(+). The lone hydrogen in the odd-numbered complexes is covalently bound atop a carbon atom but a large barrier of 1.69 eV impedes chemisorption of the H2 molecules. Calculations for neutral and doubly charged complexes are presented as well.

Decorating (C60) n+, n = 1-3, with CO2 at low temperatures: Sterically enhanced physisorption.

Multiple attachment of CO2 to the monomer, dimer and trimer cations of C60 has been observed in the mass spectra of He nanodroplets sequentially doped with C60 and CO2 and exposed to electron ionization at 50 eV. Remarkable anomalies were seen in the ion yield for CO2 coverage for (C60)2+(CO2)8 and (C60)3+(CO2)1,2. These provide insight into the influence of steric properties on the nature of physisorption. The enhanced stabilities of (C60)2+(CO2)8 and (C60)3+(CO2)1,2 are attributed to physisorption inside the "groove" of the dimer and the two "dimples" in the trimer cations of C60. Molecular dynamics simulations provide a qualitative assessment of the observed physisorption and a useful visualization of structural aspects.

Ionization of doped helium nanodroplets: complexes of C60 with water clusters.

Water clusters are known to undergo an autoprotonation reaction upon ionization by photons or electron impact, resulting in the formation of (H(2)O)(n)H(3)O(+). Ejection of OH cannot be quenched by near-threshold ionization; it is only partly quenched when clusters are complexed with inert gas atoms. Mass spectra recorded by electron ionization of water-doped helium droplets show that the helium matrix also fails to quench OH loss. The situation changes drastically when helium droplets are codoped with C(60). Charged C(60)-water complexes are predominantly unprotonated; C(60)(H(2)O)(4)(+) and (C(60))(2)(H(2)O)(4)(+) appear with enhanced abundance. Another intense ion series is due to C(60)(H(2)O)(n)OH(+); dehydrogenation is proposed to be initiated by charge transfer between the primary He(+) ion and C(60). The resulting electronically excited C(60)(+*) leads to the formation of a doubly charged C(60)-water complex either via emission of an Auger electron from C(60)(+*), or internal Penning ionization of the attached water complex, followed by charge separation within {C(60)(H(2)O)(n)}(2+). This mechanism would also explain previous observations of dehydrogenation reactions in doped helium droplets. Mass-analyzed ion kinetic energy scans reveal spontaneous (unimolecular) dissociation of C(60)(H(2)O)(n)(+). In addition to the loss of single water molecules, a prominent reaction channel yields bare C(60)(+) for sizes n=3, 4, or 6. Ab initio Hartree-Fock calculations for C(60)-water complexes reveal negligible charge transfer within neutral complexes. Cationic complexes are well described as water clusters weakly bound to C(60)(+). For n=3, 4, or 6, fissionlike desorption of the entire water complex from C(60)(H(2)O)(n)(+) energetically competes with the evaporation of a single water molecule.

Dissociative electron attachment to pentaerythritol tetranitrate: significant fragmentation near 0 eV.

Gas phase dissociative electron attachment (DEA) measurements to pentaerythritol tetranitrate (PETN) are performed in a crossed electron-molecular beam experiment at high-energy resolution and high sensitivity. DEA is operative at very low energies close to approximately 0 eV showing unique features corresponding to a variety of fragment anions being formed. There is no evidence of the parent anion formation. The fragmentation yields are also observed for higher electron energies and are operative via several resonant features in the range of 0-12 eV. In contrast to nitroaromatic compounds, PETN decays more rapidly upon electron attachment and preferentially low-mass anions are formed. The dominant fragment ion formed through DEA is assigned to the nitrogen trioxide NO(3)(-) and represents about 80% of the total anion yield. Further intense ion signals are due to NO(2)(-) (11%) and O(-) (2.5%). The significant instability of PETN after attachment of an electron with virtually no kinetic energy confers a highly explosive nature to this compound.

Metastable anions of dinitrobenzene: resonances for electron attachment and kinetic energy release.

Attachment of free, low-energy electrons to dinitrobenzene (DNB) in the gas phase leads to DNB(-) as well as several fragment anions. DNB(-), (DNB-H)(-), (DNB-NO)(-), (DNB-2NO)(-), and (DNB-NO(2))(-) are found to undergo metastable (unimolecular) dissociation. A rich pattern of resonances in the yield of these metastable reactions versus electron energy is observed; some resonances are highly isomer-specific. Most metastable reactions are accompanied by large average kinetic energy releases (KER) that range from 0.5 to 1.32 eV, typical of complex rearrangement reactions, but (1,3-DNB-H)(-) features a resonance with a KER of only 0.06 eV for loss of NO. (1,3-DNB-NO)(-) offers a rare example of a sequential metastable reaction, namely, loss of NO followed by loss of CO to yield C(5)H(4)O(-) with a large KER of 1.32 eV. The G4(MP2) method is applied to compute adiabatic electron affinities and reaction energies for several of the observed metastable channels.

Temperature effects on the dissociative electron attachment to dichlorobenzene isomers.

Dissociative electron attachment to all three isomers of dichlorobenzene has been investigated in the electron energy range from 0 to 2 eV and in the gas temperature range from 391 to 696 K using a crossed electron-molecular beam apparatus with a new temperature-regulated effusive molecular beam source. In the case of the dissociative electron attachment channel Cl(-)/1,2-dichlorobenzene and Cl(-)/1,4-dichlorobenzene, strong enhancement of the negative ion production with the gas temperature at low electron energies has been observed. The low-energy peak increases dramatically when the gas temperature is raised from 391 to 696 K. Activation energies for dissociative electron attachment of (482 +/- 20) meV for 1,2-dichlorobenzene and (59 +/- 20) meV for 1,4-dichlorobenzene have been determined. For the resonance at (0.49 +/- 0.03) eV in 1,2-dichlorobenzene and (0.32 +/- 0.03) eV in 1,4-dichlorobenzene, no dependence of the cross sections on the gas temperature has been observed. In the case of the dissociative electron attachment to Cl(-)/1,3-dichlorobenzene, the cross section does not depend on the temperature in the electron energy range from 0 to 2 eV. Quantum chemical calculations of the reaction energies and of the potential energy curves involved in the dissociation of Cl(-) have been performed, together with an analysis of the thermo dynamical accessibility of the relevant vibrational modes. Possible reasons for the different temperature dependences of the isomers are discussed.

Probing royal demolition explosive (1,3,5-trinitro-1,3,5-triazocyclohexane) by low-energy electrons: Strong dissociative electron attachment near 0 eV.

Low energy electron attachment to gas phase royal demolition explosive (RDX) (and RDX-A3) has been performed by means of a crossed electron-molecular beam experiment in an electron energy range from 0 to 14 eV with an energy resolution of approximately 70 meV. The most intense signals are observed at 102 and 46 amu and assigned to C(2)H(4)N(3)O(2) (-) and NO(2) (-), respectively. Anion efficiency curves of 16 anions have been measured. Product ions are observed mainly in the low energy region, near 0 eV arising from surprisingly complex reactions associated with multiple bond cleavages and structural and electronic rearrangement. The remarkable instability of RDX to electron attachment with virtually thermal electrons reflects the highly explosive nature of this compound. The present results are compared to other explosive aromatic nitrocompounds studied in our laboratory recently.

Formation of even-numbered hydrogen cluster cations in ultracold helium droplets.

Neutral hydrogen clusters are grown in ultracold helium nanodroplets by successive pickup of hydrogen molecules. Even-numbered hydrogen cluster cations are observed upon electron-impact ionization with and without attached helium atoms and in addition to the familiar odd-numbered H(n)(+). The helium matrix affects the fragmentation dynamics that usually lead to the formation of overwhelmingly odd-numbered H(n)(+). The use of high-resolution mass spectrometry allows the unambiguous identification of even-numbered H(n)(+) up to n approximately = 120 by their mass excess that distinguishes them from He(n)(+), mixed He(m)H(n)(+), and background ions. The large range in size of these hydrogen cluster ions is unprecedented, as is the accuracy of their definition. Apart from the previously observed magic number n=6, pronounced drops in the abundance of even-numbered cluster ions are seen at n=30 and 114, which suggest icosahedral shell closures at H(6)(+)(H(2))(12) and H(6)(+)(H(2))(54). Possible isomers of H(6)(+) are identified at the quadratic configuration interaction with inclusion of single and double excitations (QCISD)/aug-cc-pVTZ level of theory.

Fragmentation of metastable SF(6)(-*) ions with microsecond lifetimes in competition with autodetachment.

Fragmentation of metastable SF(6)(-*) ions formed in low energy electron attachment to SF(6) has been investigated. The dissociation reaction SF(6)(-*)-->SF(5) (-)+F has been observed approximately 1.5-3.4 micros and approximately 17-32 micros after electron attachment in a time-of-flight and a double focusing two sector field mass spectrometer, respectively. Metastable dissociation is observed with maximum intensity at approximately 0.3 eV between the SF(6)(-*) peak at zero and the SF(5)(-) peak at approximately 0.4 eV. The kinetic energy released in dissociation is low, with a most probable value of 18 meV. The lifetime of SF(6)(-*) decreases as the electron energy increases, but it is not possible to fit this decrease with statistical Rice-Ramsperger-Kassel/quasiequilibrium theory. Metastable dissociation of SF(6)(-*) appears to compete with autodetachment of the electron at all electron energies.

Dissociative electron attachment to gas phase glycine: exploring the decomposition pathways by mass separation of isobaric fragment anions.

Dissociative electron attachment to gas phase glycine generates a number of fragment ions, among them ions observed at the mass numbers 15, 16 and 26 amu. From stoichiometry they can be assigned to the chemically rather different species NH(-)/CH(3)(-)(15 amu), O(-)/NH(2)(-)(16 amu) and CN(-)/C(2)H(2)(-)(26 amu). Here we use a high resolution double focusing two sector mass spectrometer to separate these isobaric ions. It is thereby possible to unravel the decomposition reactions of the different transient negative ions formed upon resonant electron attachment to neutral glycine in the energy range 0-15 eV. We find that within the isobaric ion pairs, the individual components generally arise from resonances located at substantial different energies. The corresponding unimolecular decompositions involve complex reaction sequences including multiple bond cleavages and substantial rearrangement in the precursor ion. To support the interpretation and assignments we also use (13)C labelling of glycine at the carboxylic group.