"DNA at the whim of the water": Environmental DNA as a course-based undergraduate research experience.

Course-based undergraduate research experiences (CUREs) increase student access to high impact research experiences. CUREs engage students in the scientific process by learning how to pose scientific questions, develop hypotheses, and generate data to test them. Environmental DNA (eDNA), is a growing field of research that is gaining accessibility through decreasing laboratory costs, which can make a foundation for multiple, engaging CUREs. This manuscript describes three case studies that used eDNA in an upper year undergraduate course. The first focusses on a systematic literature review of eDNA metadata reporting. The second describes the biomonitoring of brook trout in southern Ontario using eDNA. The third involves eDNA metabarcoding for freshwater fish detection in southern Ontario. Undergraduates were involved in the development and execution of experiments, scientific communication, the peer review process, and fundraising. Through this manuscript, we show the novel application of eDNA CUREs and provide a roadmap for other instructors interested in implementing similar projects. Interviews with seven students from these courses indicate the benefits experienced from taking these courses. We argue that the use of eDNA in CUREs should be expanded in undergraduate biology programs due to the benefit to students and the increasing accessibility of this technology.

Caring for COVID-19 patients through a pandemic in the intensive care setting: A narrative review.

Since the declaration of the novel SARS-CoV-2 virus pandemic, health systems/ health-care-workers globally have been overwhelmed by a vast number of COVID-19 related hospitalizations and intensive care unit (ICU) admissions. During the early stages of the pandemic, the lack of formalized evidence-based guidelines in all aspects of patient management was a significant challenge. Coupled with a lack of effective pharmacotherapies resulted in unsatisfactory outcomes in ICU patients. The anticipated increment in ICU surge capacity was staggering, with almost every ICU worldwide being advised to increase their capacity to allow adequate care provision in response to multiple waves of the pandemic. This increase in surge capacity required advanced planning and reassessments at every stage, taking advantage of experienced gained in combination with emerging evidence. In University Hospital Southampton General Intensive Care Unit (GICU), despite the initial lack of national and international guidance, we enhanced our ICU capacity and developed local guidance on all aspects of care to address the rapid demand from the increasing COVID-19 admissions. The main element of this success was a multidisciplinary team approach intertwined with equipment and infrastructural reorganization. This narrative review provides an insight into the approach adopted by our center to manage patients with COVID-19 critical illness, exploring the initial planning process, including contingency preparations to accommodate (360% capacity increment) and adaptation of our management pathways as more evidence emerged throughout the pandemic to provide the most appropriate levels of care to our patients. We hope our experience will benefit other intensive care units worldwide. This article is categorized under: Infectious Diseases > Genetics/Genomics/Epigenetics.

Characterizing biological macromolecules with attenuated total reflectance-Fourier transform infrared spectroscopy provides hands-on spectroscopy experiences for undergraduates.

Infrared (IR) spectra of biologically derived materials display distinct absorption bands correlating to individual macromolecules: protein, polysaccharide, lipid, and nucleic acids. A series of experiments aimed at teaching qualitative bioorganic spectroscopy using attenuated total reflectance (ATR) Fourier transform infrared (IR) with biological polymers as samples is proposed. Labs targeting 1st and 4th year undergraduate students at St. Francis College are being developed. During 2014 âž” 2017, an integrated biology/chemistry exercise featuring elementary spectroscopy as an addition to an existing lab on light microscopy was administered to three sections of a 1st year general biology course. Students were taught the concept of a spectral fingerprint and to identify carbohydrate and protein based materials by looking for key vibrational bands. The success of that effort as determined by the results of an assessment quiz became the motivation for developing an advanced 4th year exercise involving four macromolecules. In a trial lab (Spring 2019) students gathered reference spectra from materials homogeneous in a single biopolymer followed by spectra of whole tissues which they were expected to fully characterize. Assessment data suggest that 1st year students benefited most from the experience. A detailed discussion of reference and sample spectra (as obtained by students) and relevant bond vibrations along with suggestions for instructors are presented.

Mass transfer and flow characterization of novel algae-based nutrient removal system.

BACKGROUND: Recirculating aquaculture systems (RAS) are an essential component of sustainable inland seafood production. Still, nutrient removal from these systems can result in substantial environmental problems, or present a major cost factor with few added value options. In this study, an innovative and energy-efficient algae based nutrient removal system (NRS) was developed that has the potential to generate revenue through algal commercialization. We optimized mass transfer in our NRS design using novel aeration and mixing technology, using air lift pumps and developed an original membrane cartridge for the continuous operation of nutrient removal and algae production. Specifically, we designed, manufactured and tested a 60-L NRS prototype. Based on specific airlift mixing conditions as well as concentration gradients, we assessed NRS nutrient removal capacity. We then examined the effects of different internal bioreactor geometries and radial orientations on the mixing efficiency. RESULTS: Using the start-up dynamic method, the overall mass transfer coefficient was found to be in the range of 0.00164-0.0074 [Formula: see text], depending on flow parameters and we confirmed a scaling relationship of mass transfer across concentration gradients. We found the optimal Reynolds number to be 500 for optimal mass transfer, as higher Reynolds numbers resulted in a relatively reduced increase of mass transfer. This relationship between mass transfer and Reynolds number is critical to assess scalability of our system. Our results demonstrate an even distribution of dissolved oxygen levels across the reactor core, demonstrating adequate mixing by the airlift pump, a critical consideration for optimal algal growth. Distribution of dissolved gases in the reactor was further assessed using flow visualization in order to relate the bubble distribution to the mass transfer capabilities of the reactor. We run a successful proof of principle trial using the green alga Dunaliella tertiolecta to assess mass transfer of nutrients across the membrane and biomass production. CONCLUSIONS: Manipulation of the concentration gradient across the membrane demonstrates a more prominent role of airlift mixing at higher concentration gradients. Specifically, the mass transfer rate increased threefold when the concentration gradient was increased 2.5-fold. We found that we can grow algae in the reactor chamber at rates comparable to those of other production systems and that the membrane scaffolds effectively remove nutrients form the wastewater. Our findings provide support for scalability of the design and support the use of this novel NRS for nutrient removal in aquaculture and potentially other applications.

Financial toxicity in gynecologic oncology.

OBJECTIVES: Financial toxicity is increasingly recognized as an adverse outcome of cancer treatment. Our objective was to measure financial toxicity among gynecologic oncology patients and its association with demographic and disease-related characteristics; self-reported overall health; and cost-coping strategies. METHODS: Follow-up patients at a gynecologic oncology practice completed a survey including the COmprehensive Score for Financial Toxicity (COST) tool and a self-reported overall health assessment, the EQ-VAS. We abstracted disease and treatment characteristics from medical records. We dichotomized COST scores into low and high financial toxicity and assessed the correlation (r) between COST scores and self-reported health. We calculated risk ratios (RR) and 95% confidence intervals (CI) for the associations of demographic and disease-related characteristics with high financial toxicity, as well as the associations between high financial toxicity and cost-coping strategies. RESULTS: Among 240 respondents, median COST score was 29. Greater financial toxicity was correlated with worse self-reported health (r = 0.47; p < 0.001). In the crude analysis, Black or Hispanic race/ethnicity, government-sponsored health insurance, lower income, unemployment, cervical cancer and treatment with chemotherapy were associated with high financial toxicity. In the multivariable analysis, only government-sponsored health insurance, lower income, and treatment with chemotherapy were significantly associated with high financial toxicity. High financial toxicity was significantly associated with all cost-coping strategies, including delaying or avoiding care (RR: 7.3; 95% CI: 2.8-19.1). CONCLUSIONS: Among highly-insured gynecologic oncology patients, many respondents reported high levels of financial toxicity. High financial toxicity was significantly associated with worse self-reported overall health and cost-coping strategies, including delaying or avoiding care.

Wellness in Canadian paediatric residents and their program directors.

PURPOSE: This study aimed to explore the prevalence of and identify risk factors for depression and burnout in paediatric residents and paediatric program directors (PDs) in Canada. METHODS: Residents and PDs completed separate anonymous online surveys consisting of demographic questions, the Maslach Burnout Inventory and the Patient Health Questionnaire-2, which screens for risk of depression. RESULTS: A total of 166 paediatric residents completed the survey representing 14/17 Canadian paediatric residency programs. Participants were 74% female. Twenty-four (14%) were at risk of depression and 69 (42%) met criteria for burnout. Burnout was associated with year of residency (P=0.03), with third year residents at highest risk. Residents who reported unhelpful wellness curricula were at risk of burnout (81.3%) compared with those with no wellness curricula (51.1%) or curricula reported as helpful (29.1%, P=0.01). More than 79% of residents at risk of depression also met criteria for burnout (P=0.01). No associations were identified for risk of depression.Seventeen of 21 Canadian PDs completed the survey. No PDs were identified as at risk for depression. Five PDs (29%) met criteria for burnout. CONCLUSIONS: Paediatric PDs in Canada have relatively low rates of burnout and depression. In contrast, a large number of Canadian paediatric residents met criteria for burnout. Residents in programs with wellness curricula described as helpful are at lowest risk of burnout. Future research should include identifying features that define helpful wellness curricula and exploring interventions to help residents at risk of burnout and depression.

Helping Families Cope with the Severe Stress of Dravet Syndrome.

A child with Dravet syndrome shakes family life to the core. Dravet syndrome usually has three phases: (1) up to 1-1½ years: with episodes of febrile status epilepticus but normal development; (2) age 1½ to ~6-10 years: with frequent seizures of varying types, developmental stagnation, behavioural and sleep problems; (3) after ~10 years: improvement in seizures, deteriorating gait, intellectual disability but some developmental gains. Complete seizure control is rare-simply prescribing medication is inadequate to help families. Based on structured interviews with 24 families and confirmed by more informal discussions with other families, we suggest strategies for coping with this catastrophe. A child with Dravet syndrome usually means that one parent cannot work-financial pressures should be anticipated. In Stage 1, the approach to status should include a written protocol. An indwelling catheter for rapid venous access may be helpful. In Stage 2, assistance finding qualified babysitters is required, and the extended family needs encouragement to help. Appropriate equipment, rescue medication and protocols should travel with the child. Siblings may benefit from a system of one parent "on call." An internet support group provides an invaluable lifeline. In Stage 3, family isolation may be extreme-respite care and personal time for parents are important. Death from status, accidents and SUDEP (sudden unexplained death in epilepsy) occurs in 15%. Fear of SUDEP needs to be addressed. Moving from paediatric to adult care is frightening; an epilepsy transition clinic is useful. Attention to these realities may improve the quality of life for both child and family.

Foxp3 expression is required for the induction of therapeutic tissue tolerance.

CD4(+)Foxp3(+) regulatory T cells (Treg) are essential for immune homeostasis and maintenance of self-tolerance. They are produced in the thymus and also generated de novo in the periphery in a TGF-ß-dependent manner. Foxp3(+) Treg are also required to achieve tolerance to transplanted tissues when induced by coreceptor or costimulation blockade. Using TCR-transgenic mice to avoid issues of autoimmune pathology, we show that Foxp3 expression is both necessary and sufficient for tissue tolerance by coreceptor blockade. Moreover, the known need in tolerance induction for TGF-ß signaling to T cells can wholly be explained by its role in induction of Foxp3, as such signaling proved dispensable for the suppressive process. We analyzed the relative contribution of TGF-ß and Foxp3 to the transcriptome of TGF-ß-induced Treg and showed that TGF-ß elicited a large set of downregulated signature genes. The number of genes uniquely modulated due to the influence of Foxp3 alone was surprisingly limited. Retroviral-mediated conditional nuclear expression of Foxp3 proved sufficient to confer transplant-suppressive potency on CD4(+) T cells and was lost once nuclear Foxp3 expression was extinguished. These data support a dual role for TGF-ß and Foxp3 in induced tolerance, in which TGF-ß stimulates Foxp3 expression, for which sustained expression is then associated with acquisition of tolerance.

Helping families cope with the devastation of Dravet syndrome.

Dravet syndrome shakes family life to the core. Seizure control is rarely complete, and simply prescribing medication is inadequate to help families. Our suggestions are based on structured interviews with >25 Dravet families. In Stage 1 (up to 1-1½ years), a written protocol for an organized approach to status epilepticus is mandatory. In Stage 2 (age from 1½ to ~6-10 years), assistance in finding qualified baby sitters (extended family and others) is required. Equipment, rescue medication and protocols should accompany the child. Siblings may benefit from assigning one parent to be "on call", and an Internet support group provides an invaluable lifeline. In Stage 3 (after ~10 years), family isolation may become extreme: respite care and personal time for parents are important. An epilepsy transition clinic that can effectively liaise with adult emergency services is optimal. Attention to these realities may improve the quality of life for the child and family.

Does Dravet syndrome have a recognizable face?

We hypothesized that children with Dravet syndrome manifest specific facial features that can be identified by pediatric neurologists and rendered objective by standard photographic measurements. This study comprised two parts. In Part 1, photographs of children with Dravet syndrome were compiled into a booklet with patients and their siblings randomly mixed. The booklet was sent to pediatric neurologists who anonymously identified which children they thought were affected by the syndrome and which were siblings. Although pediatric neurologists generally agreed on whether children were affected or not (20/24 cases; 83%), they were frequently incorrect (12/20; 60%). In Part 2, standard photogrammetric techniques were used to provide 16 facial ratios from digital images. No significant difference in any measurement was evident between children with Dravet syndrome and unaffected siblings (P > 0.05, two-tailed t test). This study did not demonstrate a specific facial phenotype in Dravet syndrome.

Generation of anti-inflammatory adenosine by leukocytes is regulated by TGF-ß.

Levels of anti-inflammatory extracellular adenosine are controlled by the sequential action of the ectonucleotidases CD39 and CD73, whose expression in CD4(+) T cells has been associated with natural regulatory T cells (nTregs). We here show that CD73 expression on activated murine CD4(+) T cells is induced by TGF-ß independently of Foxp3 expression, operates at the transcriptional level and translates into gain of functional capacity to generate adenosine. In the presence of AMP, CD73 induced by TGF-ß generates adenosine able to suppress proliferation of activated CD4(+) T cells in vitro. These effects are contextual and opposed by proinflammatory cytokines. CD73 is also upregulated by TGF-ß in CD8(+) T cells, DCs and macrophages, so providing an amplification mechanism for adenosine generation in tissue microenvironments. Together, these findings expose a novel anti-inflammatory role for TGF-ß.

Connecting the mechanisms of T-cell regulation: dendritic cells as the missing link.

A variety of different molecular mechanisms have been proposed to explain the suppressive action of regulatory T cells, including the production of anti-inflammatory cytokines, negative costimulatory ligands, indoleamine 2,3-dioxygenase-mediated tryptophan catabolism, CD73-mediated adenosine generation, and downregulation of antigen-presenting cells. Until now it has been unclear how important each of these different mechanisms might be and how they are coordinated. In this review, we examine the hypothesis that it is the interaction between regulatory T cells and dendritic cells that creates a local microenvironment depleted of essential amino acids and rich in adenosine that leads to the amplification of a range of different tolerogenic signals. These signals are all eventually integrated by mammalian target of rapamycin inhibition, which enables the induction of new forkhead box protein 3-expressing Tregs. If correct, this provides a molecular explanation for the in vivo phenomena of linked suppression and infectious tolerance.

Tolerogenicity is not an absolute property of a dendritic cell.

Pharmacological modulation is known to temper the immune capacity of DC, enhancing the notion that modulated Ag-bearing DC might be used therapeutically to induce tolerance. We have investigated phenotypic features shared by such DC, and queried their potential to tolerize in different settings. Immature, IL-10, TGF-beta and 1alpha,25-dihydroxyvitamin D(3)-modulated BMDC all induced tolerance to male skin in female TCR transgenic A1.RAG mice, and the modulated DC also tolerized after exposure to the TLR4-ligand LPS. Transcript profiling revealed that this was achieved despite retaining much of the normal LPS-maturation response. No shared tolerance-associated transcripts could be identified. Equivalent BMDC could not tolerize in Marilyn TCR-transgenic mice. Simultaneous presentation of both A1.RAG and Marilyn peptide-Ag (Dby-H2E(k) and Dby-H2A(b)) on immature (C57BL/6JxCBA/Ca) F1 BMDC also only achieved tolerance in A1.RAG mice. Both strains registered Ag, but Foxp3(+) Treg were only induced in A1.RAG mice. In contrast, Marilyn T cells showed greater proliferation and an inflammatory bias, in response to Ag presented by immature F1 BMDC in vitro. In summary, while pharmacological agents can skew DC to reinforce their immature tolerogenic phenotype, the outcome of presentation is ultimately an integrated response including T-cell-intrinsic components that can over-ride for immune activation.

A novel role for Glucocorticoid-Induced TNF Receptor Ligand (Gitrl) in early embryonic zebrafish development.

Tumour necrosis factor ligand and receptor superfamily (TNFSF and TNFRSF) members have diverse and well-studied functions in the immune system. Additional, non-immunological roles, such as in the morphogenesis of bone, tooth, hair and skin have also been described for some members. GITRL and its receptor GITR are well-described as co-regulators of the mammalian immune response. Here, we describe the identification and cloning of their zebrafish homologues and demonstrate a novel role for the ligand, but not the receptor, in early vertebrate development. The assignment of zebrafish Gitrl and Gitr was supported by homology and phylogenetic analysis. The ligand exhibited an oscillating pattern of mRNA expression during the first 36 hours post fertilization, during which time gitr mRNA was not detected, and morpholino oligonucleotide-mediated knock-down of gitrl, but not of gitr, resulted in disruption of early embryogenesis, most clearly revealed during gastrulation, which corresponded to the earliest peak in gitrl mRNA expression (5.25-10 hpf). We found Stat3 signalling to be altered in the gitrl-morphants, suggesting that one possible role for Gitrl during embryogenesis may be modulation of Jak/Stat signalling.

MS4A4B is a GITR-associated membrane adapter, expressed by regulatory T cells, which modulates T cell activation.

In the aftermath of thymic negative selection, natural and adaptive regulatory T cells (Tregs) must acknowledge peripheral, "danger-free" self-Ag to ensure their sustained activity. In this paper, we show that natural and adaptive Tregs or T cells transduced with cDNA for Foxp3, just like Th1 cells, express members of the MS4A family of transmembrane molecules. Naive T cells transduced with MS4A4B become able to respond to lower levels of Ag. Using two family members, MS4A4B and MS4A6B, as baits in a yeast split-ubiquitin Treg library screen, we demonstrate their interaction with each other and with GITR, Orai1, and other surface receptors. Interaction of 4B with GITR augments GITR signaling and T cell IL-2 production in response to triggering with GITR ligand or anti-GITR Abs. This interaction provides a mechanism whereby MS4A family members, through lateral coassociation with costimulatory molecules, may amplify Ag signals. We propose that T cells preoccupied with immune defense use this MS4A family to enhance sensitivity to extrinsic Ag stimulation, ensuring its elimination, while Tregs use these adaptors to allow low level Ag signals to sustain regulatory function.

Infectious tolerance via the consumption of essential amino acids and mTOR signaling.

Infectious tolerance describes the process of CD4(+) regulatory T cells (Tregs) converting naïve T cells to become additional Tregs. We show that antigen-specific Tregs induce, within skin grafts and dendritic cells, the expression of enzymes that consume at least 5 different essential amino acids (EAAs). T cells fail to proliferate in response to antigen when any 1, or more, of these EAAs are limiting, which is associated with a reduced mammalian target of rapamycin (mTOR) signaling. Inhibition of the mTOR pathway by limiting EAAs, or by specific inhibitors, induces the Treg-specific transcription factor forkhead box P3, which depends on both T cell receptor activation and synergy with TGF-beta.

Dermatological conditions in intensive care: a secondary analysis of the Intensive Care National Audit and Research Centre (ICNARC) Case Mix Programme database.

INTRODUCTION: Dermatology is usually thought of as an outpatient specialty with low mortality, however some skin conditions require intensive care. These conditions are relatively rare and hence are best studied using clinical databases or disease registries. We interrogated a large, high-quality clinical database from a national audit of adult intensive care units (ICUs), with the aim of identifying and characterising patients with dermatological conditions requiring admission to ICU. METHODS: Data were extracted for 476,224 admissions to 178 ICUs in England, Wales and Northern Ireland participating in the Case Mix Programme over the time period December 1995 to September 2006. We identified admissions with dermatological conditions from the primary and secondary reasons for admission to ICU. RESULTS: A total of 2,245 dermatological admissions were identified. Conditions included infectious conditions (e.g. cutaneous cellulitis, necrotising fasciitis), dermatological malignancies, and acute skin failure (e.g. toxic epidermal necrolysis, Stevens-Johnson syndrome and autoimmune blistering diseases). These represent 0.47% of all ICU admissions, or approximately 2.1 dermatological admissions per ICU per year. Overall mortality was 28.1% in the ICU and 40.0% in hospital. Length of stay in intensive care was longest for those with acute skin failure (median 4.7 days for ICU survivors and 5.1 days for ICU non-survivors). CONCLUSION: We have identified patients who not only require intensive care, but also dermatological care. Such patients have high mortality rates and long ICU stays within the spectrum of the UK ICU population, similar to other acute medical conditions. This highlights the importance of skin failure as a distinct entity comparable to other organ system failures.