Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified ...in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Mycobacterium tuberculosis (Mtb) encodes five type VII secretion systems (T7SS), designated ESX-1–ESX-5, that are critical for growth and pathogenesis. The best characterized is ESX-1, which ...profoundly impacts host cell interactions. In contrast, the ESX-3 T7SS is implicated in metal homeostasis, but efforts to define its function have been limited by an inability to recover deletion mutants. We overcame this impediment using medium supplemented with various iron complexes to recover mutants with deletions encompassing select genes within esx-3 or the entire operon. The esx-3 mutants were defective in uptake of siderophore-bound iron and dramatically accumulated cell-associated mycobactin siderophores. Proteomic analyses of culture filtrate revealed that secretion of EsxG and EsxH was codependent and that EsxG–EsxH also facilitated secretion of several members of the proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) protein families (named for conserved PE and PPE N-terminal motifs). Substrates that depended on EsxG–EsxH for secretion included PE5, encoded within the esx-3 locus, and the evolutionarily related PE15–PPE20 encoded outside the esx-3 locus. In vivo characterization of the mutants unexpectedly showed that the ESX-3 secretion system plays both iron-dependent and -independent roles in Mtb pathogenesis. PE5–PPE4 was found to be critical for the siderophore-mediated iron-acquisition functions of ESX-3. The importance of this iron-acquisition function was dependent upon host genotype, suggesting a role for ESX-3 secretion in counteracting host defense mechanisms that restrict iron availability. Further, we demonstrate that the ESX-3 T7SS secretes certain effectors that are important for iron uptake while additional secreted effectors modulate virulence in an iron-independent fashion.
Background A large portion of COVID-19 cases and deaths in the United States have occurred in nursing homes; however, current literature including the frontline perspective of staff working in ...nursing homes is limited. The objective of this qualitative assessment was to better understand what individual and facility level factors may have contributed to the impact of COVID-19 on Certified Nursing Assistants (CNAs) and Environmental Services (EVS) staff working in nursing homes. Methods Based on a simple random sample from the National Healthcare Safety Network (NHSN), 7,520 facilities were emailed invitations requesting one CNA and/or one EVS staff member for participation in a voluntary focus group over Zoom. Facility characteristics were obtained via NHSN and publicly available sources; participant demographics were collected via SurveyMonkey during registration and polling during focus groups. Qualitative information was coded using NVIVO and Excel. Results Throughout April 2021, 23 focus groups including 110 participants from 84 facilities were conducted homogenous by participant role. Staffing problems were a recurring theme reported. Participants often cited the toll the pandemic took on their emotional well-being, describing increased stress, responsibilities, and time needed to complete their jobs. The lack of consistent and systematic guidance resulting in frequently changing infection prevention protocols was also reported across focus groups. Conclusions Addressing concerns of low wages and lack of financial incentives may have the potential to attract and retain employees to help alleviate nursing home staff shortages. Additionally, access to mental health resources could help nursing home staff cope with the emotional burden of the COVID-19 pandemic. These frontline staff members provided invaluable insight and should be included in improvement efforts to support nursing homes recovering from the impact of COVID-19 as well as future pandemic planning.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Autophagy, TERT, and mitochondrial dysfunction in hyperoxia Beyer, Andreas M; Norwood Toro, Laura E; Hughes, William E ...
American journal of physiology. Heart and circulatory physiology,
11/2021, Letnik:
321, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Ventilation with gases containing enhanced fractions of oxygen is the cornerstone of therapy for patients with hypoxia and acute respiratory distress syndrome. Yet, hyperoxia treatment increases free ...reactive oxygen species (ROS)-induced lung injury, which is reported to disrupt autophagy/mitophagy. Altered extranuclear activity of the catalytic subunit of telomerase, telomerase reverse transcriptase (TERT), plays a protective role in ROS injury and autophagy in the systemic and coronary endothelium. We investigated interactions between autophagy/mitophagy and TERT that contribute to mitochondrial dysfunction and pulmonary injury in cultured rat lung microvascular endothelial cells (RLMVECs) exposed in vitro, and rat lungs exposed in vivo to hyperoxia for 48 h. Hyperoxia-induced mitochondrial damage in rat lungs TOMM20, 3-(4,5-dimethylthiazol-2-
)-2,5-diphenyltetrazolium bromide (MTT), which was paralleled by increased markers of inflammation myeloperoxidase (MPO), IL-1β, TLR9, impaired autophagy signaling (Beclin-1, LC3B-II/1, and p62), and decreased the expression of TERT. Mitochondrial-specific autophagy (mitophagy) was not altered, as hyperoxia increased expression of Pink1 but not Parkin. Hyperoxia-induced mitochondrial damage (TOMM20) was more pronounced in rats that lack the catalytic subunit of TERT and resulted in a reduction in cellular proliferation rather than cell death in RLMVECs. Activation of TERT or autophagy individually offset mitochondrial damage (MTT). Combined activation/inhibition failed to alleviate hyperoxic-induced mitochondrial damage in vitro, whereas activation of autophagy in vivo decreased mitochondrial damage (MTT) in both wild type (WT) and rats lacking TERT. Functionally, activation of either TERT or autophagy preserved transendothelial membrane resistance. Altogether, these observations show that activation of autophagy/mitophagy and/or TERT mitigate loss of mitochondrial function and barrier integrity in hyperoxia.
In cultured pulmonary artery endothelial cells and in lungs exposed in vivo to hyperoxia, autophagy is activated, but clearance of autophagosomes is impaired in a manner that suggests cross talk between TERT and autophagy. Stimulation of autophagy prevents hyperoxia-induced decreases in mitochondrial metabolism and sustains monolayer resistance. Hyperoxia increases mitochondrial outer membrane (TOMM20) protein, decreases mitochondrial function, and reduces cellular proliferation without increasing cell death.
Photolysis of the non-steroidal anti-inflammatory drug ibuprofen was studied by exposure to a solar simulator in solutions of fulvic acid (FA) isolated from Pony Lake, Antarctica; Suwannee River, GA, ...USA; and Old Woman Creek, OH, USA. At an initial concentration of 10 μM, ibuprofen degrades by direct photolysis, but the presence of FA significantly increases reaction rates. These reactions proceeded up to 6× faster in FA solutions at lower ibuprofen concentrations (0.1 μM), but the rates are highly dependent upon DOM composition. Incomplete quenching of the reaction in the presence of isopropanol suggests that the hydroxyl radical is only partially responsible for ibuprofen’s photodegradation in FA solutions, and other reactive transients likely play an important role. Liquid chromatography-quadrupole time-of-flight mass spectrometry and NMR spectroscopy reveal the formation of multiple photoproducts, with three byproducts identified as 1-(4-isobutylphenyl)ethanol, isobutylacetophenone, and a phenol derivative. Pony Lake FA significantly increases the production of the major byproduct relative to yields produced by direct photolysis and the other two FA. Thus, the photolytic fate of ibuprofen in sunlit waters is affected by its initial concentration and the source of dissolved organic matter present.
► Ibuprofen photodegradation occurs slowly in water and is enhanced in the presence of fulvic acids. ► The composition of fulvic acids influences ibuprofen’s transformation pathway and kinetics. ► Enhanced photoreactivity of ibuprofen at low initial concentration (0.1 μM) in the presence of fulvic acids was observed. ► Multiple photoproducts were identified including isobutylacetophenone, a precursor used in the synthesis of ibuprofen.
Objective and design
The purpose of this study was to explore pathological processes during the first 4 weeks after anterior cruciate ligament reconstruction (ACLR).
Subjects
Sixteen ACL-injured ...patients (8 females/8 males, mean age = 19.1, mean BMI = 28.6).
Methods
Arthrocentesis was performed 1 and 4 weeks after ACLR. Proteins in the synovial fluid were identified using nanoLC–ESI-MS/MS. Differentially up- or down-regulated proteins were identified and quantified, and a pathway analysis was performed. All identified proteins were mapped into a protein–protein interaction (PPI) network, and networks of PPIs with a combined score > 0.9 were then visualized.
Results
Seven pathways were upregulated after ACLR: PI3K-AKT signaling pathway, extracellular matrix (ECM)–receptor interaction, focal adhesion, protein digestion and absorption, ameobiasis, and platelet activation. Network analyses identified 8 proteins that were differentially upregulated with strong PPI interactions (periostin and 7 collagen-related proteins). Increases in periostin moderately correlated with increases in a synovial fluid biomarker of type II cartilage degradation (
ρ
= 0.51,
p
= 0.06).
Conclusion
Pro-inflammatory pathways and periostin were upregulated after ACLR. Periostin demonstrated strong network connections with markers of collagen breakdown, and future work is needed to determine whether periostin may offer a biomarker of early cartilage degradation after ACLR and/or play an active role in early post-traumatic osteoarthritis (PTOA) progression.
Mixed lineage kinase domain-like pseudokinase (MLKL), a key terminal effector of necroptosis, also plays a role in intracellular vesicle trafficking that is critical for regulating liver inflammation ...and injury in alcohol-associated liver disease (ALD). Although receptor interacting protein kinase 3 (Rip3)-/- mice are completely protected from ethanol-induced liver injury, Mlkl-/- mice are only partially protected. Therefore, we hypothesized that cell-specific functions of MLKL may contribute to ethanol-induced injury.
Bone marrow transplants between Mlkl-/- mice and littermates were conducted to distinguish the role of myeloid versus nonmyeloid Mlkl in the Gao-binge model of ALD. Ethanol-induced hepatic injury, steatosis, and inflammation were exacerbated in Mlkl-/- →wild-type (WT) mice, whereas Mlkl deficiency in nonmyeloid cells (WT→ Mlkl-/- ) had no effect on Gao-binge ethanol-induced injury. Importantly, Mlkl deficiency in myeloid cells exacerbated ethanol-mediated bacterial burden and accumulation of immune cells in livers. Mechanistically, challenging macrophages with lipopolysaccharide (LPS) induced signal transducer and activator of transcription 1-mediated expression and phosphorylation of MLKL, as well as translocation and oligomerization of MLKL to intracellular compartments, including phagosomes and lysosomes but not plasma membrane. Importantly, pharmacological or genetic inhibition of MLKL suppressed the phagocytic capability of primary mouse Kupffer cells (KCs) at baseline and in response to LPS with/without ethanol as well as peripheral monocytes isolated from both healthy controls and patients with alcohol-associated hepatitis. Further, in vivo studies revealed that KCs of Mlkl-/- mice phagocytosed fewer bioparticles than KCs of WT mice.
Together, these data indicate that myeloid MLKL restricts ethanol-induced liver inflammation and injury by regulating hepatic immune cell homeostasis and macrophage phagocytosis.
Peer-supported mobile health (mhealth) programs hold the promise of providing a low-burden approach to increasing access to care and improving mental health. While peer support has been shown to ...improve engagement into care, there is limited investigation about the impact of peers on symptom outcome. Trauma-exposed populations frequently suffer from co-occurring posttraumatic stress and depressive symptoms as well as difficulties in day-to-day functioning. This study evaluated the potential benefits of a peer-supported transdiagnostic mhealth program on symptom outcomes and functioning.BACKGROUNDPeer-supported mobile health (mhealth) programs hold the promise of providing a low-burden approach to increasing access to care and improving mental health. While peer support has been shown to improve engagement into care, there is limited investigation about the impact of peers on symptom outcome. Trauma-exposed populations frequently suffer from co-occurring posttraumatic stress and depressive symptoms as well as difficulties in day-to-day functioning. This study evaluated the potential benefits of a peer-supported transdiagnostic mhealth program on symptom outcomes and functioning.This randomized controlled trial tested the effectiveness of Brief Peer-Supported (BPS) webSTAIR, a 6-module transdiagnostic online program derived from Skills Training in Affective and Interpersonal Regulation (STAIR) compared to waitlist control (WL) in a community sample of Veterans who screened positive for either post-traumatic stress disorder (PTSD) and/or depression.OBJECTIVEThis randomized controlled trial tested the effectiveness of Brief Peer-Supported (BPS) webSTAIR, a 6-module transdiagnostic online program derived from Skills Training in Affective and Interpersonal Regulation (STAIR) compared to waitlist control (WL) in a community sample of Veterans who screened positive for either post-traumatic stress disorder (PTSD) and/or depression.A total of 178 eligible Veterans were enrolled in the study using a 2:1 randomization scheme with 117 assigned to BPS webSTAIR and 61 assigned to WL. PTSD and depressive symptoms as well as emotion regulation, and psychosocial functioning were assessed via phone at pretreatment, posttreatment, and 8-week follow-up. Mixed-effects models were used to assess change in outcome measures across timepoints and evaluate the impact of module completion on outcomes. Exploratory analyses were conducted to determine whether the type and number of peer interactions influenced outcomes.METHODSA total of 178 eligible Veterans were enrolled in the study using a 2:1 randomization scheme with 117 assigned to BPS webSTAIR and 61 assigned to WL. PTSD and depressive symptoms as well as emotion regulation, and psychosocial functioning were assessed via phone at pretreatment, posttreatment, and 8-week follow-up. Mixed-effects models were used to assess change in outcome measures across timepoints and evaluate the impact of module completion on outcomes. Exploratory analyses were conducted to determine whether the type and number of peer interactions influenced outcomes.Significant interaction effects were observed for all outcomes such that participants randomized to BPS webSTAIR reported significantly greater improvement at posttreatment compared to WL with moderate effect sizes for PTSD (PCL-5 d = -0.48) depression (PHQ- 8 d = -0.64), emotion regulation (DERS-16 d = 0.61) and functional impairment (WSAS d = 0.61); gains were maintained at 8-week follow-up. Those who completed more modules reported greater improvement on all outcomes. An initial cohort of participants who were required to engage with a peer coach to progress through the modules interacted more frequently with peers but completed fewer modules compared to a later cohort for whom peer engagement was optional.RESULTSSignificant interaction effects were observed for all outcomes such that participants randomized to BPS webSTAIR reported significantly greater improvement at posttreatment compared to WL with moderate effect sizes for PTSD (PCL-5 d = -0.48) depression (PHQ- 8 d = -0.64), emotion regulation (DERS-16 d = 0.61) and functional impairment (WSAS d = 0.61); gains were maintained at 8-week follow-up. Those who completed more modules reported greater improvement on all outcomes. An initial cohort of participants who were required to engage with a peer coach to progress through the modules interacted more frequently with peers but completed fewer modules compared to a later cohort for whom peer engagement was optional.BPS webSTAIR was effective in improving PTSD and depression symptoms, emotion regulation, and psychosocial functioning in community Veterans. Peer-supported transdiagnostic mhealth programs may be a particularly efficient, effective, and low-burden approach to improving mental health among trauma-exposed populations. Investigation of peer-supported programs among other populations is necessary to evaluate the generalizability of the findings. Analyses comparing peer support that was required versus optional indicated that some veterans may not need or want peer support. Future research should evaluate how best to deliver peer support and for whom it is most beneficial. If successful, peer-supported tech programs may increase the VA workforce as well as improve veteran mental health services and outcomes.CONCLUSIONSBPS webSTAIR was effective in improving PTSD and depression symptoms, emotion regulation, and psychosocial functioning in community Veterans. Peer-supported transdiagnostic mhealth programs may be a particularly efficient, effective, and low-burden approach to improving mental health among trauma-exposed populations. Investigation of peer-supported programs among other populations is necessary to evaluate the generalizability of the findings. Analyses comparing peer support that was required versus optional indicated that some veterans may not need or want peer support. Future research should evaluate how best to deliver peer support and for whom it is most beneficial. If successful, peer-supported tech programs may increase the VA workforce as well as improve veteran mental health services and outcomes.ClinicalTrials.gov NCT04286165.CLINICALTRIALClinicalTrials.gov NCT04286165.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Oomycete pathogens are commonly associated with soybean root rot and have been estimated to reduce soybean yields in the United States by 1.5 million tons on an annual basis. Limited information ...exists regarding the frequency and diversity of oomycete species across the major soybean-producing regions in North America. A survey was conducted across 11 major soybean-producing states in the United States and the province of Ontario, Canada. In 2011, 2,378 oomycete cultures were isolated from soybean seedling roots on a semiselective medium (CMA-PARPB) and were identified by sequencing of the internal transcribed spacer region of rDNA. Sequence results distinguished a total of 51 Pythium spp., three Phytophthora spp., three Phytopythium spp., and one Aphanomyces sp. in 2011, with Pythium sylvaticum (16%) and P. oopapillum (13%) being the most prevalent. In 2012, the survey was repeated, but, due to drought conditions across the sampling area, fewer total isolates (n = 1,038) were collected. Additionally, in 2012, a second semiselective medium (V8-RPBH) was included, which increased the Phytophthora spp. isolated from 0.7 to 7% of the total isolates. In 2012, 54 Pythium spp., seven Phytophthora spp., six Phytopythium spp., and one Pythiogeton sp. were recovered, with P. sylvaticum (14%) and P. heterothallicum (12%) being recovered most frequently. Pathogenicity and virulence were evaluated with representative isolates of each of the 84 species on soybean cv. Sloan. A seed-rot assay identified 13 and 11 pathogenic species, respectively, at 13 and 20°C. A seedling-root assay conducted at 20°C identified 43 species as pathogenic, having a significantly detrimental effect on the seedling roots as compared with the noninoculated control. A total of 15 species were pathogenic in both the seed and seedling assays. This study provides a comprehensive characterization of oomycete species present in soybean seedling roots in the major production areas in the United States and Ontario, Canada and provides a basis for disease management and breeding programs.
Soybean (Glycine max (L.) Merr.) is produced across a vast swath of North America, with the greatest concentration in the Midwest. Root rot diseases and damping-off are a major concern for ...production, and the primary causal agents include oomycetes and fungi. In this study, we focused on examination of oomycete species distribution in this soybean production system and how environmental and soil (edaphic) factors correlate with oomycete community composition at early plant growth stages. Using a culture-based approach, 3,418 oomycete isolates were collected from 11 major soybean-producing states and most were identified to genus and species using the internal transcribed spacer region of the ribosomal DNA. Pythium was the predominant genus isolated and investigated in this study. An ecology approach was taken to understand the diversity and distribution of oomycete species across geographical locations of soybean production. Metadata associated with field sample locations were collected using geographical information systems. Operational taxonomic units (OTU) were used in this study to investigate diversity by location, with OTU being defined as isolate sequences with 97% identity to one another. The mean number of OTU ranged from 2.5 to 14 per field at the state level. Most OTU in this study, classified as Pythium clades, were present in each field in every state; however, major differences were observed in the relative abundance of each clade, which resulted in clustering of states in close proximity. Because there was similar community composition (presence or absence) but differences in OTU abundance by state, the ordination analysis did not show strong patterns of aggregation. Incorporation of 37 environmental and edaphic factors using vector-fitting and Mantel tests identified 15 factors that correlate with the community composition in this survey. Further investigation using redundancy analysis identified latitude, longitude, precipitation, and temperature as factors that contribute to the variability observed in community composition. Soil parameters such as clay content and electrical conductivity also affected distribution of oomycete species. The present study suggests that oomycete species composition across geographical locations of soybean production is affected by a combination of environmental and edaphic conditions. This knowledge provides the basis to understand the ecology and distribution of oomycete species, especially those able to cause diseases in soybean, providing cues to develop management strategies.
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