Omega 3 Fatty Acids Promote Macrophage Reverse Cholesterol Transport in Hamster Fed High Fat Diet

The aim of this study was to investigate macrophage reverse cholesterol transport (RCT) in hamster, a CETP-expressing species, fed omega 3 fatty acids (ω3PUFA) supplemented high fat diet (HFD). Three groups of hamsters (n = 6/group) were studied for 20 weeks: 1) control diet: Control, 2) HFD group: HF and 3) HFD group supplemented with ω3PUFA (EPA and DHA): HFω3. In vivo macrophage-to-feces RCT was assessed after an intraperitoneal injection of ³H-cholesterol-labelled hamster primary macrophages.Compared to Control, HF presented significant (p<0.05) increase in body weight, plasma TG (p<0.01) and cholesterol (p<0.001) with an increase in VLDL TG and in VLDL and LDL cholesterol (p<0.001).Compared to HF, HFω3 presented significant decrease in body weight. HFω3 showed less plasma TG (p<0.001) and cholesterol (p<0.001) related to a decrease in VLDL TG and HDL cholesterol respectively and higher LCAT activity (p<0.05) compared to HF. HFω3 showed a higher fecal bile acid excretion (p<0.05) compared to Control and HF groups and higher fecal cholesterol excretion (p<0.05) compared to HF. This increase was related to higher gene expression of ABCG5, ABCA1 and SR-B1 in HFω3 compared to Control and HF groups (<0.05) and in ABCG1 and CYP7A1 compared to HF group (p<0.05). A higher plasma efflux capacity was also measured in HFω3 using ³H- cholesterol labeled Fu5AH cells.In conclusion, EPA and DHA supplementation improved macrophage to feces reverse cholesterol transport in hamster fed HFD. This change was related to the higher cholesterol and fecal bile acids excretion and to the activation of major genes involved in RCT.     

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.     

A novel nuclear export signal and a REF interaction domain both promote mRNA export by the Epstein-Barr virus EB2 protein

A striking characteristic of mRNA export factors is that they shuttle continuously between the cytoplasm and the nucleus. This shuttling is mediated by specific factors interacting with peptide motifs called nuclear export signals (NES) and nuclear localization signals. We have identified a novel CRM-1-independent transferable NES and two nuclear localization signals in the Epstein-Barr virus mRNA export factor EB2 (also called BMLF1, Mta, or SM) localized at the N terminus of the protein between amino acids 61 and 146. We have also found that a previously described double NES (amino acids 213-236) does not mediate the nuclear shuttling of EB2, but is an interaction domain with the cellular export factor REF in vitro. This newly characterized REF interaction domain is essential for EB2-mediated mRNA export. Accordingly, in vivo, EB2 is found in complexes containing REF as well as the cellular factor TAP. However, these interactions are RNase-sensitive, suggesting that the RNA is an essential component of these complexes.     

Studies on the primary sequence requirements for PKC-alpha, -beta 1 and -gamma peptide substrates.

The substrate specificity of purified PKC-alpha, -beta and -gamma has been investigated. A series of synthetic peptides based upon the sequence surrounding serine-7 in glycogen synthase were generated and used to determine the basic residue requirements of these PKC isotypes. While PKC-alpha and -beta are indistinguishable in their phosphorylation of these peptides, PKC-gamma shows a distinct specificity profile for these synthetic substrates.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

Long-Lasting Immune Protection and Other Epidemiological Findings after Chikungunya Emergence in a Cambodian Rural Community,April 2012

The East/Central/South African genotype of Chikungunya virus with the E1-A226V mutation emerged in 2011 in Cambodia and spread in 2012. An outbreak of 190 cases was documented in Trapeang Roka, a rural village. We surveyed 425 village residents within 3–4 weeks after the outbreak, and determined the sensitivity and specificity of case definitions and factors associated with infection by CHIKV. Self-reported clinical presentation consisted mostly of fever, rash and arthralgia. The presence of all three clinical signs or symptoms was identified as the most sensitive (67%) and specific (84%) self-reported diagnostic clinical indicator compared to biological confirmation by MAC-ELISA or RT-PCR used as a reference. Having an indoor occupation was associated with lower odds of infection compared with people who remained at home (adjOR 0.32, 95%CI 0.12–0.82). In contrast with findings from outbreaks in other settings, persons aged above 40 years were less at risk of CHIKV infection, likely reflecting immune protection acquired when Chikungunya circulated in Cambodia before the Khmer Rouge regime in 1975. In view of the very particular history of Cambodia, our epidemiological data from Trapeang Roka are the first to support the persistence of CHIKV antibodies over a period of 40 years.     

Diagnoses and factors associated with medical evacuation and return to duty among nonmilitary personnel participating in military operations in Iraq and Afghanistan

Background

Nonmilitary personnel play an increasingly critical role in modern wars. Stark differences exist between the demographic characteristics, training and missions of military and nonmilitary members. We examined the differences in types of injury and rates of returning to duty among nonmilitary and military personnel participating in military operations in Iraq and Afghanistan.

Methods

We collected data for nonmilitary personnel medically evacuated from military operations in Iraq and Afghanistan between 2004 and 2007. We compared injury categories and return-to-duty rates in this group with previously published data for military personnel and identified factors associated with return to duty.

Results

Of the 2155 medically evacuated nonmilitary personnel, 74.7% did not return to duty. War-related injuries in this group accounted for 25.6% of the evacuations, the most common causes being combat-related injuries (55.4%) and musculoskeletal/spinal injuries (22.9%). Among individuals with non–war-related injuries, musculoskeletal injuries accounted for 17.8% of evacuations. Diagnoses associated with the highest return-to-duty rates in the group of nonmilitary personnel were psychiatric diagnoses (15.6%) among those with war-related injuries and noncardiac chest or abdominal pain (44.0%) among those with non–war-related injuries. Compared with military personnel, nonmilitary personnel with war-related injuries were less likely to return to duty (4.4% v. 5.9%, p = 0.001) but more likely to return to duty after non–war-related injuries (32.5% v. 30.7%, p = 0.001).

Interpretation

Compared with military personnel, nonmilitary personnel were more likely to be evacuated with non–war-related injuries but more likely to return to duty after such injuries. For evacuations because of war-related injuries, this trend was reversed.In modern warfare, injuries sustained in combat have never been the leading source of attrition among soldiers. In World War I, World War II and the Korean War, respiratory and infectious diseases were the top reasons for hospital admissions among service members. By the Vietnam Conflict, non-battle injuries had supplanted respiratory illness as the leading cause of hospital admissions and have remained the leading cause ever since.^1,2The principal causes for medical evacuation of military personnel from US operations in Iraq and Afghanistan were recently described in a large four-year epidemiologic study.³ In descending order, the leading reasons were musculoskeletal conditions, combat-related injuries, neurologic symptoms and psychiatric disorders; the last category surpassed combat-related injuries as the number two reason in the latter half of both engagements. However, nonmilitary personnel were not included in that study. Over the past three years, nonmilitary members, including US Department of Defense civilians, private contractors and diplomats, have comprised about 50% of personnel serving in Iraq and about two-thirds of those serving in Afghanistan.^4,5Several reasons may explain why the types of injury and the return-to-duty rates differ between military and nonmilitary personnel. First, the motivations for overseas deployment might differ between the groups. Whereas some civilian personnel (e.g., diplomats) may be assigned to positions in Iraq and Afghanistan, virtually all private contractors volunteer for their jobs. In contrast, most military members have little choice in their deployment. Second, military and nonmilitary members assigned to war zones have different occupational specialties, living conditions and regulations to which they must adhere. Especially for junior military personnel, jobs tend to be more dangerous, living environments more austere and regulations more stringent. Finally, unlike military personnel, who are paid regardless of deployment status, most contractors’ pay is contingent upon continued employment in theatres of operation. In addition, nonmilitary personnel are generally compensated with higher salaries than service members in comparable occupational specialties.In civilian cohorts, many of these factors have been shown to influence return-to-work rates in a variety of contexts. Studies of the effect of financial compensation on work status after injury have generally shown a direct correlation between return-to-work rates and higher income levels.^6,7 Similar associations have also been found between return-to-work rates and job satisfaction and coping mechanisms, factors that may be influenced by work conditions and perceived control over one’s environment.^8–10The objectives of our study were threefold: to ascertain whether the reasons for medical evacuation from military operations differed between military and nonmilitary personnel; to determine whether return-to-duty rates differed between the two groups; and to identify factors that influence return-to-duty rates among nonmilitary members.     

Activation of oxidative metabolism of granulocytes and monocytes by IGG-coated platelets from patients with thrombocytopenia

We have previously shown that monoclonal anti-T cell antibodies bound to their specific targets can trigger the activation of monocyte/macrophage oxidative metabolism through an Fc receptor-mediated interaction. The present study demonstrates that IgG coated platelets from patients with thrombocytopenia-associated diseases can induce a similar respiratory burst activation in polymorphonuclear and mononuclear phagocytes from normal individuals. The intensity of the oxidative reaction as measured by luminol-dependent chemiluminescence is in close correlation with the level of surface-bound IgG molecules as determined by a radioactive anti-immunoglobulin assay. This new methodology to evaluating IgG fixed on human platelets by their capacity to trigger the generation of highly reactive oxygen species by granulocytes and monocytes has also suggested a new mechanism in the genesis of thrombocytopenia associated with autoimmune diseases.