EEF1A2 pathogenic variant presenting in an infant with failure to thrive and frequent apneas requiring respiratory support.

EEF1A2 is a gene whose protein product, eukaryotic translation elongation factor 1 alpha 2 (eEF1A2), plays an important role in neurodevelopment. Reports of individuals with pathogenic variants in EEF1A2 are rare, with less than 40 individuals reported world-wide, however a common feature is the association of the variant with developmental and epileptic encephalopathy. Thus far, there have been limited reports of other organ systems or body functions affected by variants in this gene. Here, we present a case of a child with EEF1A2-related disorder who presented at 3 months of age with hypotonia, microcephaly, failure to thrive, and respiratory insufficiency with central apneas requiring respiratory support. Our case highlights the notion that the respiratory system may be highly implicated in EEF1A2-related disorder, allowing for better phenotypic characterization of the disorder.

Evaluation of three commercial PCR kits for the direct detection of Mycobacterium avium subsp. paratuberculosis (MAP) in bovine faeces.

Mycobacterium avium subsp. paratuberculosis which is more commonly referred to as MAP is the causative agent of Johnes's disease in ruminants. While cultivation of MAP from faecal samples remains the reference standard diagnostic test for the disease, faecal culture is expensive, slow and not widely available in Ireland. The current study evaluated three commercial kits that combine both DNA extraction and real-time PCR amplification of specific targets for direct MAP detection in cattle faeces. In total, 100 positive samples were tested which consisted of 25 high shedders, 25 medium shedders, 25 low shedders and 25 very low shedders. Also included were 100 negative faecal samples obtained from two Irish herds known to be free of Johne's disease. The kits evaluated in this study showed significant differences in identifying MAP DNA from animals shedding various concentrations of the bacterium. Kit C had the highest specificity, followed by kits B and A. Sensitivity in kits A, B and C was 73.5%, 81% and 93%, respectively, and specificity was 99%, 97% and 100%, respectively. Sensitivity decreased with lower concentrations of MAP in faeces but this was more significant for kits A and B than for kit C. The results of this study demonstrate that PCR can provide an accurate and rapid detection of MAP faecal shedding and kit C was selected for further evaluation of the role of PCR in the confirmation of animal infection in cattle.

Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.

Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double-mutant strains, does not scale readily to multi-condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG-GI), by which double-mutant strains generated via en masse "party" mating can also be monitored en masse for growth to detect genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53.

Corpus callosum shape and morphology in youth across the psychosis Spectrum.

The corpus callosum is the largest white matter tract in the human brain connecting and coordinating homologous regions of the right and left hemispheres and has been strongly implicated in the pathogenesis of psychosis. We investigated corpus callosum morphology in a large community cohort of 917 individuals (aged 8-21), including 267 endorsing subsyndromal or threshold psychotic symptoms (207 on the psychosis spectrum and 60 with limited psychosis based on previously published criteria) and 650 non-psychotic volunteers. We used a highly reliable and previously published algorithm to automatically identify the midsagittal plane and to align the corpus callosum along the anterior and posterior commissures for segmentation, thereby eliminating these sources of error variance in dependent measures, which included perimeter, length, mean thickness and shape (circularity). The parcellation scheme divided the corpus callosum into 7 subregions that consisted of the rostrum, genu, rostral body, anterior midbody, posterior midbody, isthmus, and splenium. Both individuals endorsing psychotic symptoms and those with limited psychosis had significantly (p<.05) smaller area and lower thickness measures compared to healthy volunteers, but did not differ significantly from each other. Findings were relatively widespread indicating a relatively global effect not circumscribed to any particular corpus callosum subregion. These data are consistent with the hypothesis that corpus callosum abnormalities may be evident early in the course of illness and predate the onset of frank psychosis. Given that these measures can be easily obtained and are highly reliable they may assist in the identification of individuals at future risk for psychosis.

Soft X-Ray Second Harmonic Generation as an Interfacial Probe.

Nonlinear optical processes at soft x-ray wavelengths have remained largely unexplored due to the lack of available light sources with the requisite intensity and coherence. Here we report the observation of soft x-ray second harmonic generation near the carbon K edge (∼284 eV) in graphite thin films generated by high intensity, coherent soft x-ray pulses at the FERMI free electron laser. Our experimental results and accompanying first-principles theoretical analysis highlight the effect of resonant enhancement above the carbon K edge and show the technique to be interfacially sensitive in a centrosymmetric sample with second harmonic intensity arising primarily from the first atomic layer at the open surface. This technique and the associated theoretical framework demonstrate the ability to selectively probe interfaces, including those that are buried, with elemental specificity, providing a new tool for a range of scientific problems.

Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.

OBJECTIVE: To examine linkages between mitochondrial genetics and preterm birth by assessing the risk for preterm birth associated with the inheritance of nuclear haplotypes that are ancestrally distinct from mitochondrial haplogroup. STUDY DESIGN: Genome-wide genotyping studies of cohorts of preterm and term individuals were evaluated. We determined the mitochondrial haplogroup and nuclear ancestry for individuals and developed a scoring for the degree to which mitochondrial ancestry is divergent from nuclear ancestry. RESULTS: Infants with higher degrees of divergent mitochondrial ancestry were at increased risk for preterm birth (0.124 for preterm vs 0.105 for term infants; P< .05). This finding was validated in 1 of 2 replication cohorts. We also observed that greater degrees of divergent ancestry correlated with earlier delivery within the primary study population, but this finding was not replicated in secondary cohorts born preterm. CONCLUSIONS: Individuals with divergent patterns of mitochondrial and nuclear ancestry are at increased risk for preterm birth. These findings may in part explain the higher rates of preterm birth in African Americans and in individuals with a matrilineal family history of preterm birth.

Strain and Bond Length Dynamics upon Growth and Transfer of Graphene by NEXAFS Spectroscopy from First-Principles and Experiment.

As the quest toward novel materials proceeds, improved characterization technologies are needed. In particular, the atomic thickness in graphene and other 2D materials renders some conventional technologies obsolete. Characterization technologies at wafer level are needed with enough sensitivity to detect strain in order to inform fabrication. In this work, NEXAFS spectroscopy was combined with simulations to predict lattice parameters of graphene grown on copper and further transferred to a variety of substrates. The strains associated with the predicted lattice parameters are in agreement with experimental findings. The approach presented here holds promise to effectively measure strain in graphene and other 2D systems at wafer levels to inform manufacturing environments.

Determining crystal phase purity in c-BP through X-ray absorption spectroscopy.

We employ X-ray absorption near-edge spectroscopy at the boron K-edge and the phosphorus L2,3-edge to study the structural properties of cubic boron phosphide (c-BP) samples. The X-ray absorption spectra are modeled from first-principles within the density functional theory framework using the excited electron core-hole (XCH) approach. A simple structural model of a perfect c-BP crystal accurately reproduces the P L2,3-edge, however it fails to describe the broad and gradual onset of the B K-edge. Simulations of the spectroscopic signatures in boron 1s excitations of intrinsic point defects and the hexagonal BP crystal phase show that these additions to the structural model cannot reproduce the broad pre-edge of the experimental spectrum. Calculated formation enthalpies show that, during the growth of c-BP, it is possible that amorphous boron phases can be grown in conjunction with the desired boron phosphide crystalline phase. In combination with experimental and theoretically obtained X-ray absorption spectra of an amorphous boron structure, which have a similar broad absorption onset in the B K-edge spectrum as the cubic boron phosphide samples, we provide evidence for the presence of amorphous boron clusters in the synthesized c-BP samples.

Measurement of Electron-Ion Relaxation in Warm Dense Copper.

Experimental investigation of electron-ion coupling and electron heat capacity of copper in warm and dense states are presented. From time-resolved x-ray absorption spectroscopy, the temporal evolution of electron temperature is obtained for non-equilibrium warm dense copper heated by an intense femtosecond laser pulse. Electron heat capacity and electron-ion coupling are inferred from the initial electron temperature and its decrease over 10 ps. Data are compared with various theoretical models.

Mitochondria-acting hexokinase II peptides carried by short-length carbon nanotubes with increased cellular uptake, endosomal evasion, and enhanced bioactivity against cancer cells.

Type II hexokinase (HKII) has emerged as a viable therapeutic target due to its involvement in metabolic reprogramming and also apoptosis prevention. The peptide derived from the fifteen amino acid sequence in the HKII N-terminal region [HKII(pep)] can compete with endogenous proteins for binding on mitochondria and trigger apoptosis. However, this peptide is not cell-permeable. In this study, multi-walled carbon nanotubes (MWCNTs) were used to effectively deliver HKII(pep) across cellular barriers without compromising their bioactivity. The peptide was conjugated on either oxidized MWCNTs or 2,2'-(ethylenedioxy)bis(ethylamine)-functionalized MWCNTs, yielding MWCNT-HKII(pep) and MWCNT-TEG-HKII(pep), respectively. Both conjugates were shown to be internalized by breast cancer MCF-7 cells using confocal microscopy. Moreover, these nanoconjugates seemed to have escaped from endosomes and be in the vicinity of mitochondria. The WST-1 cytotoxicity assay conducted on MCF-7 and colon carcinoma HCT116 cells revealed that MWCNT-peptide conjugates were significantly more effective in curbing cancer cell growth compared to a commercially available cell permeable HKII fusion peptide. In addition, both nanoconjugates displayed an enhanced ability in eliciting apoptosis and depleting the ATP level in HCT116 cells compared to the mere HKII peptide. Importantly, hexokinase II release from mitochondria was demonstrated in MWCNT-HKII(pep) and MWCNT-TEG-HKII(pep) treated cells, highlighting that the structure and bioactivity of HKII(pep) were not compromised after covalent conjugation to MWCNTs.

Ultrafast dynamics. Attosecond band-gap dynamics in silicon.

Electron transfer from valence to conduction band states in semiconductors is the basis of modern electronics. Here, attosecond extreme ultraviolet (XUV) spectroscopy is used to resolve this process in silicon in real time. Electrons injected into the conduction band by few-cycle laser pulses alter the silicon XUV absorption spectrum in sharp steps synchronized with the laser electric field oscillations. The observed ~450-attosecond step rise time provides an upper limit for the carrier-induced band-gap reduction and the electron-electron scattering time in the conduction band. This electronic response is separated from the subsequent band-gap modifications due to lattice motion, which occurs on a time scale of 60 ± 10 femtoseconds, characteristic of the fastest optical phonon. Quantum dynamical simulations interpret the carrier injection step as light-field-induced electron tunneling.

Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012.

Genotyping of important medical or veterinary prokaryotes has become a very important tool during the last decades. Rapid development of fragment-separation and sequencing technologies has made many new genotyping strategies possible. Among these new methods is multilocus variable-number tandem repeat analysis (MLVA). Here we present an update on the use of MLVA in eight European countries (Denmark, France, Germany, Ireland, Italy, the Netherlands, Norway and Sweden). Researchers in Europe have been active in developing and implementing a large array of different assays. MLVA has been used as a typing tool in several contexts, from aiding in resolving outbreaks of foodborne bacteria to typing organisms that may pose a bioterrorist threat, as well as in scientific studies.

Psychosocial and functional correlates of nutrition among community-dwelling older adults in Ireland.

OBJECTIVES: To examine psychosocial and functional correlates of nutrition in a nonrandom sample of Irish community-dwelling older adults. DESIGN: Cross-sectional observational study. SETTING: Technology Research for Independent Living (TRIL) Clinic, a comprehensive geriatric assessment facility in St James's Hospital, Dublin. Data were collected from participants by medical personnel (physical assessments) and psychologists (questionnaires), between August 2007 and May 2009. PARTICIPANTS: 556 participants (388 females; 168 males) ranging in age from 60-92 years (Mean 72.5 years, SD 7.1). All were community-dwelling and provided informed consent. MEASUREMENTS: The Nestlé Mini-Nutritional Assessment (MNA®), Time to get up and go (TUG) and the Lubben Social Network Scale-18 (LSNS-18) were used to assess nutrition, functional mobility and social support. METHODS: Multivariate binary logistic regression was used to examine the association between social support or mobility and nutritional status, whilst controlling for possible confounders (age, gender, living alone and material deprivation). RESULTS: The strongest predictors of abnormal nutritional status were mobility (p < 0.001) and social support (p = 0.005). Other significant predictors of nutritional risk were age (p = 0.032) and deprivation (p = 0.018). CONCLUSION: The results emphasise the importance of mobility and social supports in mediating nutritional outcomes in Irish community-dwelling older adults.

Application of multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing to subtype Salmonella enterica serovar Typhimurium isolated from pig farms, pork slaughterhouses and meat producing plants in Ireland.

Salmonella enterica subsp. enterica serovar Typhimurium is a common zoonotic pathogen encountered in Irish pigs and the pork industry and its characterisation using highly discriminatory typing methods is necessary for epidemiological studies, outbreak investigation and control. Multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing were applied to characterise 301 S. typhimurium isolates of porcine origin isolated from farms, slaughterhouses and pork meat producing plants in Ireland over a four-year period. 154 MLVA patterns were obtained compared to 19 phage types and 38 AMR patterns, and MLVA was particularly useful for discriminating isolates of the same phage type, e.g. DT104 and DT104b, or isolates that were Untypable or in the category of "react with phage but does not conform to a recognised phage type" (RDNC) by the phage typing method. Cluster analysis of MLVA profiles using a minimum spanning tree (MST) demonstrated two major clusters (I and II), which showed to have a clear association with phage types, cluster I associated to phage types DT104, U302 and DT120 and cluster II associated to DT193 and U288. The results of this present study showed that MLVA is highly discriminatory and permitted the identification of identical profiles among isolates obtained at different points of the pork food chain. The same MLVA profile was observed in some cases among isolates with different phage types. While this can be explained by the fact that some phage types are closely related, it also indicates that combining phage typing and MLVA enhances strain typing of S. typhimurium.

Electronic structure of warm dense copper studied by ultrafast x-ray absorption spectroscopy.

We use time-resolved x-ray absorption spectroscopy to investigate the unoccupied electronic density of states of warm dense copper that is produced isochorically through the absorption of an ultrafast optical pulse. The temperature of the superheated electron-hole plasma, which ranges from 4000 to 10 000 K, was determined by comparing the measured x-ray absorption spectrum with a simulation. The electronic structure of warm dense copper is adequately described with the high temperature electronic density of state calculated by the density functional theory. The dynamics of the electron temperature is consistent with a two-temperature model, while a temperature-dependent electron-phonon coupling parameter is necessary.

The influence of storing beef aerobically or in vacuum packs on the shelf life of mince.

AIMS: To investigate the influence of aerobic or vacuum pack storage of beef trimmings on the microbiology, colour and odour of subsequently produced mince. METHODS AND RESULTS: Trimmings stored aerobically for 7 or 10 days and in vacuum packs for 7, 10, 14 or 22 days at 0 or 5°C were minced, stored aerobically at 0 or 5°C for up to 7 days and examined daily to determine Total viable, Pseudomonas, Lactic acid bacteria, Brochothrix thermosphacta, and Enterobacteriaceae counts, colour and odour. Mincing reduced counts, particularly of Pseudomonas, B. thermosphacta and Enterobacteriaceae, probably because of the action free radicals released from muscle and bacterial cells. Storage of vacuum-packed trimmings for 22 days resulted in improved mince colour and inhibition of the growth of Pseudomonas. CONCLUSIONS: The shelf life of mince from trimmings is directly influenced by the trimmings storage conditions, and longer-term vacuum storage of trimmings produced improvements in mince quality. SIGNIFICANCE AND IMPACT OF THE STUDY: There appears to be no scientific rationale for limiting the storage of vacuum packaging beef trimmings to 15 days, prior to mince production, as stated in EU 835/2004. This study identifies advantages in storing trimmings in vacuum packs for at least 21 days prior to mincing, in terms of improved mince quality.

Survival of Pseudomonas fluorescens on beef carcass surfaces in a commercial abattoir.

The influence of a commercial chilling process (18 h at 10 degrees C followed by up to 78 h at 2 degrees C) on Pseudomonas fluorescens inoculated on beef carcass surfaces at four sites, neck (NE), outside round (OR), brisket (BR) and foreshank/brisket (FB) before chilling ("hot inoculated") or after chilling for 24h ("cold inoculated") was investigated. Pseudomonas counts increased significantly at all sites on "hot inoculated" carcasses during storage, but on "cold inoculated" carcasses, counts declined or remained unchanged. On hot and cold inoculated carcasses, differences in Pseudomonas growth or survival were demonstrated between sites. No clear relationships were observed between Pseudomonas growth or survival and chiller relative humidity (RH) or surface water activity (a(w)) at the different sites. These results were unexpected, and are discussed in relation to environmental factors that affect the growth/survival of P. fluorescens on carcass surfaces during chilling i.e. temperature, RH, and the relationship of these parameters to surface water activity (a(w)).

Tracking the Salmonella status of pigs and pork from lairage through the slaughter process in the Republic of Ireland.

Salmonella Typhimurium is the predominant serotype isolated from humans in Europe. Pork and pork products are recognized vehicles of Salmonella and are responsible for outbreaks of human salmonellosis. Pigs can become infected with Salmonella on the breeding or fattening farm and during transport, lairage, and slaughter. The aim of this study was to investigate selected points of Salmonella contamination from the time pigs entered the lairage to the time the carcass was processed in the boning hall and to determine the importance of different sources of Salmonella along the Irish pork production chain. A second objective was to evaluate whether the serological status or category of a herd influenced the levels of bacteriological contamination detected on individual carcasses and pork cuts during slaughter and dressing operations. All samples were tested for the presence and numbers of Salmonella. Enterobacteriaceae numbers were also determined. Serotype, phage type, and pulsed-field gel electrophoresis were utilized to determine similarity among Salmonella isolates. Lairage was a major source of cross-contamination with Salmonella as were the hands of evisceration operatives, conveyor belts, and equipment in the boning hall. Cross-contamination within the slaughter plant environment accounted for up to 69 % of Salmonella carcass contamination. In general, herd category reflected the bacteriological status of carcasses and pork cuts. Major findings were a strong association (P < 0.01) between Enterobacteriaceae counts and Salmonella occurrence on prechill carcasses and a significant association (P < 0.05) between Enterobacteriaceae counts and Salmonella occurrence on pork cut samples.

Changes in Escherichia coli O157:H7 numbers during holding on excised lean, fascia and fat beef surfaces at different temperatures.

AIM: To investigate changes in Escherichia coli O157:H7 numbers on excised beef carcass surfaces over 72 h at different temperatures. METHODS AND RESULTS: Excised lean meat, fascia and fat were inoculated with E. coli O157:H7 and held in an environmental chamber for 72 h, at air speed 0.5 m s(-1), relative humidity (RH) 90%, and temperatures 4, 8 and 12 degrees C. On lean, pathogen counts increased significantly at 12 degrees C. On fascia, significant reductions in counts occurred at 4 and 8 degrees C. Pathogen numbers were significantly reduced on fat at 4, 8 and 12 degrees C (64 h). Counts on fat were significantly less at all temperatures, compared to lean or fascia and surface water activity, a(w), decreased significantly over time on fat at 4 degrees C. Significant decreases in surface pH values were recorded on all meat substrates. CONCLUSIONS: The survival of E. coli O157:H7 varied in relation to the meat substrate and the holding temperature. Reductions in counts on fat surfaces appeared to be related to low surface a(w) values. No relationship between pathogen survival and surface pH was established. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of excised meat pieces in an environmental cabinet offers a more flexible approach to determining the use of different chilling regimes in the production of safe meat.