Evaluation of the capacity and effective angle of thalamic damage for two commercially available captive bolt tool types on cadaver heads from sows > 200 kg body weight.

This study evaluated the ability of two penetrating captive bolt (PCB) types (PISTOL, INLINE) to reach and disrupt the thalamus when applied in two placements (FRONTAL, BEHIND EAR) to chilled cadaver heads (N=60) from sows > 200 kg. Heads were randomly distributed across six treatments (n=10): FRONTAL-INLINE, FRONTAL-PISTOL, FRONTAL-NO SHOT, BEHIND EAR-INLINE, BEHIND EAR-PISTOL, and BEHIND EAR-NO SHOT. The FRONTAL shot was placed 3.5 cm superior to the optic orbits at the midline; the BEHIND EAR shot was placed directly caudal to the pinna of the ear on the same plane as the eyes and targeting the middle of the opposite eye. For INLINE treatments, a Jarvis PAS-Type C 0.25R Super Heavy Duty PCB with a Long Bolt and 6.0 GR power loads was used. For PISTOL treatments, a Jarvis PAS-Type P 0.25R Pistol PCB with a Long Stunning Rod Nosepiece Assembly and 3.5 GR power loads was used. Heads were split along the bolt with a band saw. Tissue depth measurements are reported as Mean ± SE followed by 97.5% one-sided upper reference limit (URL). Total tissue thickness was less (P < 0.0001) at the FRONTAL (56.31±1.76 mm; URL: 73.17 mm) than the BEHIND EAR placement (95.52±3.30 mm; URL: 126.53 mm). Thalamic depth was less (P < 0.0001) at the FRONTAL (78.31±1.32 mm; URL: 88.19 mm) than the BEHIND EAR placement (111.86±3.22 mm; URL: 135.99 mm). Effective angle was greater (P < 0.0001) at the FRONTAL (4.72±0.20°) than the BEHIND EAR placement (3.22±0.17°). Potential for bolt-brain contact was not different (P = 1.0000) between FRONTAL-INLINE (10/10, 100±0.01%), FRONTAL-PISTOL (10/10, 100±0.01%), BEHIND EAR-INLINE (9/10, 90±9.49%), and BEHIND EAR-PISTOL (10/10, 100±0.01%); brain damage (P = 0.5577) between FRONTAL-INLINE (9/9, 100±0.02%), FRONTAL-PISTOL (10/10, 100±0.02%), BEHIND EAR-INLINE (4/10, 40±15.49%), and BEHIND EAR-PISTOL (1/10, 10±9.49%); potential for bolt-thalamus contact (P = 0.0683) for FRONTAL-INLINE (2/10, 20±12.65%), FRONTAL-PISTOL (8/10, 80±12.65%), BEHIND EAR-INLINE (7/9, 77.78±13.86%), and BEHIND EAR-PISTOL (9/9, 100±0.02%); or thalamic damage (P = 0.8041) for FRONTAL-INLINE (1/10, 10±9.49%), FRONTAL-PISTOL (1/10, 10±9.49%), BEHIND EAR-INLINE (2/8, 25±15.31%), and BEHIND EAR-PISTOL (0/9, 0±0.00%). The FRONTAL placement with an INLINE PCB may present the least risk of failure for the PCB euthanasia of mature sows > 200 kg BW due to less total tissue thickness and thalamic depth, greater effective angle, and prevalent brain damage.

Host defense peptides human ß defensin 2 and LL-37 ameliorate murine necrotizing enterocolitis.

Necrotizing enterocolitis (NEC) is a leading cause of preterm infant morbidity and mortality. Treatment for NEC is limited and non-targeted, which makes new treatment and prevention strategies critical. Host defense peptides (HDPs) are essential components of the innate immune system and have multifactorial mechanisms in host defense. LL-37 and hBD2 are two HDPs that have been shown in prior literature to protect from neonatal sepsis-induced mortality or adult inflammatory bowel disease, respectively. Therefore, this article sought to understand if these two HDPs could influence NEC severity in murine preclinical models. NEC was induced in P14-16 C57Bl/6 mice and HDPs were provided as a pretreatment or treatment. Both LL-37 and hBD2 resulted in decreased NEC injury scores as a treatment and hBD2 as a pretreatment. Our data suggest LL-37 functions through antimicrobial properties, while hBD2 functions through decreases in inflammation and improvement of intestinal barrier integrity.

Relationship of tissue dimensions and three captive bolt application sites on cadaver heads from mature swine (Sus scrofa domesticus) <200 kg body weight.

Penetrating captive bolt (PCB) is a common method of euthanasia for swine but has not been evaluated for mature swine < 200 kg body weight (BW). The objectives were to determine tissue depth, brain contact plane, and visible brain tissue damage (brain damage[BD]) for the common FRONTAL (F) and alternative TEMPORAL (T) and BEHIND EAR (BE) placements for PCB use on sows and boars weighing < 200 kg. Cadaver heads were obtained from 30 sows and 30 boars (estimated BW, mean ±â€…SD; sows: 165.8 ±â€…22.4 kg; boars: 173.6 ±â€…21.4 kg) from a slaughter establishment after electrical stunning and exsanguination. Heads were cooled at 2 to 4 °C for approximately 64 h. A Jarvis PAS-Type P 0.25R PCB with a Long Stunning Rod Nosepiece Assembly and a 3.5 GR power load was used for all PCB applications at the following placements: F-3.5 cm superior to the optic orbits at midline, T-at the depression posterior to the lateral canthus of the eye within the plane between the lateral canthus and the base of the ear, or BE-directly caudal to the pinna of the ear on the same plane as the eyes and targeting the middle of the opposite eye. For sows, the bolt path was in the brain for 10/10 (100.0%, 95% CI: 69.2% to 100.0%) F, T, and BE heads. In heads that could reliably be assessed for BD, BD was detected in 10/10 (100.0%, 95% CI: 69.2% to 100.0%) F heads, 9/9 (100.0%, 95% CI: 66.4% to 100.0%) T heads, and 0/10 (0.0%, 95% CI: 0.0% to 30.1%) BE heads. For boars, the bolt path was in the plane of the brain for 8/9 (88.9%, 95% CI: 51.8% to 99.7%) F heads, 9/10 (90.0%, 95% CI: 55.5% to 99.7%) T heads, and 11/11 (100.0%, 95% CI: 71.5% to 100.0%) BE heads. In heads that could reliably be assessed for BD, BD was detected in 8/9 (88.9%, 95% CI: 51.7% to 99.7%) F heads, 7/10 (70.0%, 95% CI: 34.8% to 93.3%) T heads, and 4/11 (36.4%, 95% CI: 10.9% to 69.2%) BE heads. Tissue depth was reported as mean ±â€…SE followed by 95% one-sided upper reference limit (URL). For sows, total tissue thickness differed (P < 0.05) between placements (F: 49.41 ±â€…2.74 mm, URL: 70.0 mm; T: 62.83 ±â€…1.83 mm, URL: 76.6 mm; BE: 84.63 ±â€…3.67 mm; URL: 112.3 mm). Total tissue thickness differed (P < 0.05) between placements for boars (F: 54.73 ±â€…3.23 mm, URL: 77.6 mm; T: 70.72 ±â€…3.60 mm, URL: 96.3 mm; BE: 92.81 ±â€…5.50 mm; URL: 135.3 mm). For swine between 120 and 200 kg BW, the F placement may have the greatest likelihood for successful euthanasia due to the least total tissue thickness and may present less risk for failure than the T and BE placements.

Euthanasia is an important procedure to protect animal welfare and cannot be avoided on swine farms. A common method of euthanasia for swine is penetrating captive bolt (PCB), which involves passing a metal bolt through the skull into the brain. This process should result in an immediate loss of consciousness. The use of PCB has been evaluated for market hogs and heavier sows and boars, but not for sows and boars weighing < 200 kg. As pigs mature, the cranial thickness at the common frontal PCB placement increases due to the expansion of sinus cavities. This makes PCB euthanasia more challenging for sows and boars. As a result, alternative PCB application sites, including behind the ear and at a temporal location, have been proposed. This study evaluated frontal, temporal, and behind-ear placements for PCB application to cadaver heads from sows and boars weighing < 200 kg. The frontal placement appeared to be more reliable than the temporal or behind ear placements due to the least tissue for the bolt to travel through to reach the brain, the greatest potential target area, and prevalent brain damage.

Ventilator Management in Extremely Preterm Infants.

Advances in ventilation strategies for infants in the NICU have led to increased survival of extremely preterm infants. More than 75% of infants born at less than or equal to 27 weeks' gestation require initial mechanical ventilation for survival due to developmental immaturity of their lungs and respiratory drive. Various ventilators using different technologies and involving multiple management strategies are available for use in this population. Centers across the world have successfully used conventional, high-frequency oscillatory and high-frequency jet ventilation to manage respiratory failure in extremely preterm infants. This review explores the existing evidence for each mode of ventilation and the importance of individualizing ventilator management strategies when caring for extremely preterm infants.

Survival and short-term respiratory outcomes of <750 g infants initially intubated with 2.0 mm vs. 2.5 mm endotracheal tubes.

OBJECTIVES: To compare survival and short-term respiratory outcomes of infants weighing <750 g initially intubated with 2.0 mm versus 2.5 mm endotracheal tube (ETT). STUDY DESIGN: Retrospective, observational cohort study. RESULTS: Of 149 inborn infants weighing <750 g admitted to the NICU, 69 (46%) were intubated with 2.0 mm ETT, 78 with 2.5 mm ETT (53%), and 2 infants never required intubation. Infants intubated with 2.0 mm ETT were more premature (median gestational age (GA) 23 weeks (22, 24) vs. 24 weeks (24, 25) p < 0.0001), smaller (median birth weight 545 g (450, 616) vs. 648 g (579, 700), p < 0.0001), and more frequently intubated at delivery (96% vs. 68%, p < 0.00001). Survival to discharge was similar 77%, 53/69 and 87%, 68/78 (p = 0.09). Adjusted for GA, there were no significant differences in ventilator days (p = 0.7338) or Grade 3 BPD. CONCLUSIONS: Premature infants born at a median GA of 23 weeks and median birth weight of 545 g can be successfully managed with 2.0 mm ETT.

Relationship of tissue dimensions and three captive bolt placements on cadaver heads from mature swine (Sus scrofa domesticus) > 200 kg body weight.

Three penetrating captive bolt (PCB) placements were tested on cadaver heads from swine with estimated body weight (BW) >200 kg (sows = 232.9 ± 4.1 kg; boars = 229.3 ± 2.6 kg). The objectives were to determine tissue depth, cross-sectional brain area, visible brain damage (BD), regions of BD, and bolt-brain contact; and determine relationships between external head dimensions and tissue depth at each placement. A Jarvis PAS-Type P 0.25R PCB with a Long Stunning Rod Nosepiece Assembly and 3.5 g power loads was used at the following placements on heads from 111 sows and 46 boars after storage at 2 to 4 °C for ~62 h before treatment: FRONTAL (F)-3.5 cm superior to the optic orbits at midline, TEMPORAL (T)-at the depression posterior to the lateral canthus of the eye within the plane between the lateral canthus and the base of the ear, or BEHIND EAR (BE)-directly caudal to the pinna of the ear on the same plane as the eyes and targeting the middle of the opposite eye. For sows, the bolt path was in the plane of the brain for 42/42 (100%, 95% confidence interval [CI]: 91.6% to 100.0%) F heads, 39/40 (97.5%, 95% CI: 86.8% to 99.9%) T heads, and 34/39 (87.5%, 95% CI: 72.6% to 95.7%) BE heads; for the heads that could reliably be assessed for BD damage was detected in 25/26 (96.2%, 95% CI: 80.4% to 99.9%) F heads, 24/35 (68.6%, 95% CI: 50.7% to 83.2%) T heads, and 5/40 (12.5%, 95% CI: 4.2% to 26.8%) BE heads. For boars, the bolt path was in the plane of the brain for 17/17 (100.0%, 95% CI: 80.5% to 100.0%) F heads, 18/18 (100.0%, 95% CI: 81.5% to 100.0%) T heads, and 14/14 (100.0%, 95% CI: 76.8% to 100.0%) BE heads; damage was detected in 11/12 (91.7%, 95% CI: 61.5% to 99.8%) F heads, 2/15 (13.3%, 95% CI: 1.7% to 40.5%) T heads, and 7/14 (50.0%, 95% CI: 23.0% to 77.0%) BE heads. Tissue depth was reported as mean ± standard error followed by 95% one-sided upper reference limit (URL). For sows, total tissue thickness was different (P < 0.05) between placements (F: 52.7 ± 1.0 mm, URL: 64.1 mm; T: 69.8 ± 1.4 mm, URL: 83.9 mm; BE: 89.3 ± 1.5 mm, URL: 103.4 mm). In boars, total tissue thickness was different (P < 0.05) between placements (F: 41.2 ± 2.1 mm, URL: 56.3 mm; T: 73.2 ± 1.5 mm, URL: 83.4 mm; BE: 90.9 ± 3.5 mm, URL: 113.5 mm). For swine > 200 kg BW, F placement may be more effective than T or BE due to less soft tissue thickness, which may reduce concussive force. The brain was within the plane of bolt travel for 100% of F heads with BD for 96.2% and 91.7% of F sow and boar heads, respectively.

The gammaherpesvirus 68 viral cyclin facilitates expression of LANA.

Gammaherpesviruses establish life-long infections within their host and have been shown to be the causative agents of devastating malignancies. Chronic infection within the host is mediated through cycles of transcriptionally quiescent stages of latency with periods of reactivation into detectable lytic and productive infection. The mechanisms that regulate reactivation from latency remain poorly understood. Previously, we defined a critical role for the viral cyclin in promoting reactivation from latency. Disruption of the viral cyclin had no impact on the frequency of cells containing viral genome during latency, yet it remains unclear whether the viral cyclin influences latently infected cells in a qualitative manner. To define the impact of the viral cyclin on properties of latent infection, we utilized a viral cyclin deficient variant expressing a LANA-beta-lactamase fusion protein (LANA::ßla), to enumerate both the cellular distribution and frequency of LANA gene expression. Disruption of the viral cyclin did not affect the cellular distribution of latently infected cells, but did result in a significant decrease in the frequency of cells that expressed LANA::ßla across multiple tissues and in both immunocompetent and immunodeficient hosts. Strikingly, whereas the cyclin-deficient virus had a reactivation defect in bulk culture, sort purified cyclin-deficient LANA::ßla expressing cells were fully capable of reactivation. These data emphasize that the γHV68 latent reservoir is comprised of at least two distinct stages of infection characterized by differential LANA expression, and that a primary function of the viral cyclin is to promote LANA expression during latency, a state associated with ex vivo reactivation competence.

CXCL14 suppresses human papillomavirus-associated head and neck cancer through antigen-specific CD8+ T-cell responses by upregulating MHC-I expression.

Evasion of the host immune responses is critical for both persistent human papillomavirus (HPV) infection and associated cancer progression. We have previously shown that expression of the homeostatic chemokine CXCL14 is significantly downregulated by the HPV oncoprotein E7 during cancer progression. Restoration of CXCL14 expression in HPV-positive head and neck cancer (HNC) cells dramatically suppresses tumor growth and increases survival through an immune-dependent mechanism in mice. Although CXCL14 recruits natural killer (NK) and T cells to the tumor microenvironment, the mechanism by which CXCL14 mediates tumor suppression through NK and/or T cells remained undefined. Here we report that CD8+ T cells are required for CXCL14-mediated tumor suppression. Using a CD8+ T-cell receptor transgenic model, we show that the CXCL14-mediated antitumor CD8+ T-cell responses require antigen specificity. Interestingly, CXCL14 expression restores major histocompatibility complex class I (MHC-I) expression on HPV-positive HNC cells downregulated by HPV, and knockdown of MHC-I expression in HNC cells results in loss of tumor suppression even with CXCL14 expression. These results suggest that CXCL14 enacts antitumor immunity through restoration of MHC-I expression on tumor cells and promoting antigen-specific CD8+ T-cell responses to suppress HPV-positive HNC.

The Hedgehog target Gli1 is not required for bleomycin-induced lung fibrosis.

Sonic Hedgehog (SHH) signaling, a developmental pathway promoting lung mesenchymal expansion and differentiation during embryogenesis, has been increasingly recognized as a profibrotic factor in mature lung, where it might contribute to the pathogenesis of lung fibrosis. Pathway inhibition at the level of the downstream Gli transcription factors Gli1 and Gli2 (by GANT61) ameliorates lung fibrosis in the bleomycin model, whereas inhibition proximally at the level of HH ligand (by anti Hh antibody 5E1) or Smo (by GDC-0449) of the canonical pathway does not, implicating Gli1 and/or Gli2 as a key target. The fact that both the Gli1-labelled cell lineage and Gli1 expressing cells expand during fibrosis formation and contribute significantly to the pool of myofibroblasts in the fibrosis scars suggests a fibrogenic role for Gli1. Therefore to further dissect the roles of Gli1 and Gli2 in lung fibrosis we evaluated Gli1 KO and control mice in the bleomycin model. Monitoring of Gli1+/+ (n = 12), Gli1lZ/+ (n = 37) and Gli1lZ/lZ (n = 18) mice did not reveal differences in weight loss or survival. Lung evaluation at the 21-day endpoint did not show differences in lung fibrosis formation (as judged by morphology and trichrome staining), Ashcroft score, lung collagen content, lung weight, BAL protein content or BAL cell differential count. Our data suggest that Gli1 is not required for bleomycin-induced lung fibrosis.

Dithizone-induced Paneth cell disruption significantly decreases intestinal perfusion in the murine small intestine.

PURPOSE: Necrotizing enterocolitis is associated with decreased intestinal perfusion and ischemia. Paneth cells, specialized epithelial cells, have been shown to regulate the intestinal vasculature and disruption of these cells has been associated with NEC. We hypothesized that Paneth cell disruption in immature mice intestine would decrease the perfusion of the intestinal microvasculature. METHODS: Paneth cells were disrupted in P14-16 mice using chemical (dithizone) and transgenic (diphtheria toxin) methodology. Six hours after Paneth cell disruption, Dylight 488 was injected directly into the left ventricle and allowed to perfuse for 5 minutes prior to intestinal harvesting. Tissue samples were evaluated with confocal fluorescence microscopy to quantify intestinal perfusion and samples were quantified by real time RT-PCR for gene expression. RESULTS: Dithizone treatment significantly decreased intestinal perfusion compared to controls (p < 0.01). However, diphtheria toxin treatment demonstrated no significant difference in perfusion (p > 0.21). Intestines from all treatment groups had similar PECAM staining, but intestines treated with dithizone had significantly decreased nNOS and iNOS gene expression compared to controls (p < 0.007). CONCLUSIONS: Paneth cell disruption significantly decreases the perfusion of the small intestinal microvasculature in a dithizone-specific manner. Dithizone has no effect on the amount of microvasculature, but does impact genes critical to nitric oxide signaling likely contributing to mesenteric vasoconstriction.

Compliance of Parenting Magazines Advertisements with American Academy of Pediatrics Recommendations.

This study examined 3218 advertisements from the two parenting magazines with highest circulation in the United States. The authors compared each advertisement for a product for use by children, against all the published recommendations of the American Academy of Pediatrics (AAP) on topics such as toy safety, helmet use, age-defined choking hazards, infant sleep safety, and others. Any advertisement with images or products which went against a published AAP recommendation was deemed as non-adherence and was categorized according to the statement it contradicted. Nearly one in six (15.7%) of the advertisements contained example(s) of non-adherence to AAP recommendations, with twelve categories of offense represented. Categories ranked by overall share from most to least include: non-Food and Drug Administration (FDA) approved medical treatments, age-defined choking hazards, vitamins, cold medicine, formula, oral care, screen time, toy/playground safety, infant sleep, nutrition, water safety, and fall risk. Given that repeated exposure to messages in advertisements has been associated with changes in health decision-making, and parents often turn to parenting magazines for advice and ideas regarding their children, the publishers might consider screening the content in order to prevent confusing and potentially dangerous messages from being disseminated in the media.

Measurements of extinct fission products in nuclear bomb debris: Determination of the yield of the Trinity nuclear test 70 y later.

This paper describes an approach to measuring extinct fission products that would allow for the characterization of a nuclear test at any time. The isotopic composition of molybdenum in five samples of glassy debris from the 1945 Trinity nuclear test has been measured. Nonnatural molybdenum isotopic compositions were observed, reflecting an input from the decay of the short-lived fission products (95)Zr and (97)Zr. By measuring both the perturbation of the (95)Mo/(96)Mo and (97)Mo/(96)Mo isotopic ratios and the total amount of molybdenum in the Trinity nuclear debris samples, it is possible to calculate the original concentrations of the (95)Zr and (97)Zr isotopes formed in the nuclear detonation. Together with a determination of the amount of plutonium in the debris, these measurements of extinct fission products allow for new estimates of the efficiency and yield of the historic Trinity test.

Suppression of Antitumor Immune Responses by Human Papillomavirus through Epigenetic Downregulation of CXCL14.

UNLABELLED: High-risk human papillomaviruses (HPVs) are causally associated with multiple human cancers. Previous studies have shown that the HPV oncoprotein E7 induces immune suppression; however, the underlying mechanisms remain unknown. To understand the mechanisms by which HPV deregulates host immune responses in the tumor microenvironment, we analyzed gene expression changes of all known chemokines and their receptors using our global gene expression data sets from human HPV-positive and -negative head/neck cancer and cervical tissue specimens in different disease stages. We report that, while many proinflammatory chemokines increase expression throughout cancer progression, CXCL14 is dramatically downregulated in HPV-positive cancers. HPV suppression of CXCL14 is dependent on E7 and associated with DNA hypermethylation in the CXCL14 promoter. Using in vivo mouse models, we revealed that restoration of Cxcl14 expression in HPV-positive mouse oropharyngeal carcinoma cells clears tumors in immunocompetent syngeneic mice, but not in Rag1-deficient mice. Further, Cxcl14 reexpression significantly increases natural killer (NK), CD4(+) T, and CD8(+) T cell infiltration into the tumor-draining lymph nodes in vivo In vitro transwell migration assays show that Cxcl14 reexpression induces chemotaxis of NK, CD4(+) T, and CD8(+) T cells. These results suggest that CXCL14 downregulation by HPV plays an important role in suppression of antitumor immune responses. Our findings provide a new mechanistic understanding of virus-induced immune evasion that contributes to cancer progression. IMPORTANCE: Human papillomaviruses (HPVs) are causally associated with more than 5% of all human cancers. During decades of cancer progression, HPV persists, evading host surveillance. However, little is known about the immune evasion mechanisms driven by HPV. Here we report that the chemokine CXCL14 is significantly downregulated in HPV-positive head/neck and cervical cancers. Using patient tissue specimens and cultured keratinocytes, we found that CXCL14 downregulation is linked to CXCL14 promoter hypermethylation induced by the HPV oncoprotein E7. Restoration of Cxcl14 expression in HPV-positive cancer cells clears tumors in immunocompetent syngeneic mice, but not in immunodeficient mice. Mice with Cxcl14 reexpression show dramatically increased natural killer and T cells in the tumor-draining lymph nodes. These results suggest that epigenetic downregulation of CXCL14 by HPV plays an important role in suppressing antitumor immune responses. Our findings may offer novel insights to develop preventive and therapeutic tools for restoring antitumor immune responses in HPV-infected individuals.

Myeloid Cell Arg1 Inhibits Control of Arthritogenic Alphavirus Infection by Suppressing Antiviral T Cells.

Arthritogenic alphaviruses, including Ross River virus (RRV) and chikungunya virus (CHIKV), are responsible for explosive epidemics involving millions of cases. These mosquito-transmitted viruses cause inflammation and injury in skeletal muscle and joint tissues that results in debilitating pain. We previously showed that arginase 1 (Arg1) was highly expressed in myeloid cells in the infected and inflamed musculoskeletal tissues of RRV- and CHIKV-infected mice, and specific deletion of Arg1 from myeloid cells resulted in enhanced viral control. Here, we show that Arg1, along with other genes associated with suppressive myeloid cells, is induced in PBMCs isolated from CHIKV-infected patients during the acute phase as well as the chronic phase, and that high Arg1 expression levels were associated with high viral loads and disease severity. Depletion of both CD4 and CD8 T cells from RRV-infected Arg1-deficient mice restored viral loads to levels detected in T cell-depleted wild-type mice. Moreover, Arg1-expressing myeloid cells inhibited virus-specific T cells in the inflamed and infected musculoskeletal tissues, but not lymphoid tissues, following RRV infection in mice, including suppression of interferon-γ and CD69 expression. Collectively, these data enhance our understanding of the immune response following arthritogenic alphavirus infection and suggest that immunosuppressive myeloid cells may contribute to the duration or severity of these debilitating infections.

Chemodiversity in the fingerprint analysis of volatile organic compounds (VOCs) of 35 old and 7 modern apple cultivars determined by proton-transfer-reaction mass spectrometry (PTR-MS) in two different seasons.

Volatile organic compounds (VOCs) are chemical species that play an important role in determining the characteristic aroma and flavor of fruits. Apple (Malus × domestica Borkh.) cultivars differ in their aroma and composition of VOCs. To determine varietal differences in the aroma profiles, VOCs emitted by 7 modern and 35 old apple cultivars were analyzed using Proton Transfer Reaction Mass Spectrometry (PTR-MS). PTR-MS is a rapid, reproducible, and non-destructive spectrometric technique for VOC analysis of single fruits, developed for direct injection analysis. In the present study, we analyzed the differences in the emission of VOCs from single fruits at harvest and after a storage period of 60±10 days, followed by 3 d of shelf life. Our results show that VOC profile differences among apple cultivars were more pronounced after storage than at harvest. Furthermore, chemodiversity was higher in old cultivars compared to modern cultivars, probably due to their greater genetic variability. Our data highlight the importance of storage and shelf life are crucial for the development of the typical aroma and flavor of several apple cultivars. The validity of the method is demonstrated by comparison of two different harvest years.

The use of δ13C isotope ratio mass spectrometry for methamphetamine profiling: comparison of ephedrine and pseudoephedrine-based samples to P2P-based samples.

Differentiating methamphetamine samples produced from ephedrine and pseudoephedrine from phenyl-2-propanone precursors is critical for assigning synthetic route information for methamphetamine profiling. The use of isotope ratio mass spectrometry data is now a key component for tracking precursor information. Recent carbon (δ(13)C) isotope results from the analysis of numerous methamphetamine samples show clear differentiation for ephedrine and pseudoephedrine-produced samples compared to P2P-produced samples. The carbon isotope differences were confirmed from synthetic route precursor studies.

SRmapper: a fast and sensitive genome-hashing alignment tool.

UNLABELLED: Modern sequencing instruments have the capability to produce millions of short reads every day. The large number of reads produced in conjunction with variations between reads and reference genomic sequences caused both by legitimate differences, such as single-nucleotide polymorphisms and insertions/deletions (indels), and by sequencer errors make alignment a difficult and computationally expensive task, and many reads cannot be aligned. Here, we introduce a new alignment tool, SRmapper, which in tests using real data can align 10s of billions of base pairs from short reads to the human genome per computer processor day. SRmapper tolerates a higher number of mismatches than current programs based on Burrows-Wheeler transform and finds about the same number of alignments in 2-8× less time depending on read length (with higher performance gain for longer read length). The current version of SRmapper aligns both single and pair-end reads in base space fastq format and outputs alignments in Sequence Alignment/Map format. SRmapper uses a probabilistic approach to set a default number of mismatches allowed and determines alignment quality. SRmapper's memory footprint (∼2.5 GB) is small enough that it can be run on a computer with 4 GB of random access memory for a genome the size of a human. Finally, SRmapper is designed so that its function can be extended to finding small indels as well as long deletions and chromosomal translocations in future versions. AVAILABILITY: http://www.umsl.edu/∼wongch/software.html.

Diphenylamine residues in apples caused by contamination in fruit storage facilities.

The potential of fruit storage facilities that are contaminated with the widely used chemical antioxidant diphenylamine to cross-contaminate untreated apples (Malus × domestica Borkh.) was studied. A new sample preparation method identified the storage room paint, contaminated from past treatments, as the major source of cross-contamination in the analyzed facilities. Diphenylamine amounts of up to 917 g were found in a single storage room and were shown to correlate with the extent of cross-contamination on stored apples. Our data support a diffusion-based mechanism where the wall paint releases the antioxidant to the storage room atmosphere even years after the last treatment. Given the extent of cross-contamination found in our model experiments and under commercial storage conditions, we deduce a significant risk of exceeding the potentially upcoming maximum residue level of 0.01 mg kg(-1) on stored fruit in contaminated rooms even years after the last diphenylamine treatment.