Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics.

The emergence of robust single-cell 'omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell 'omics approaches show: 1) the description of the ciliates in the class Karyorelictea as "primitive" is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani's (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages

Plant-pollinator interactions over 120 years: loss of species, co-occurrence, and function

Using historic data sets, we quantified the degree to which global change over 120 years disrupted plant-pollinator interactions in a temperate forest understory community in Illinois, USA. We found degradation of interaction network structure and function and extirpation of 50% of bee species. Network changes can be attributed to shifts in forb and bee phenologies resulting in temporal mismatches, nonrandom species extinctions, and loss of spatial co-occurrences between extant species in modified landscapes. Quantity and quality of pollination services have declined through time. The historic network showed flexibility in response to disturbance; however, our data suggest that networks will be less resilient to future changes

Preterm prelabour rupture of membranes before 23 weeks' gestation: prospective observational study

Objective To describe perinatal and maternal outcomes of preterm prelabour rupture of membranes (PPROM) before 23 weeks' gestation in a national cohort. Design Prospective observational study. Setting National population based cohort study with the UK Obstetric Surveillance System (UKOSS), a research infrastructure of all 194 obstetric units in the UK, 1 September 2019 to 28 February 2021. Participants 326 women with singleton and 38 with multiple pregnancies with PPROM between 16+0 and 22+6 weeks+days' gestation. Main outcome measures Perinatal outcomes of live birth, survival to discharge from hospital, and severe morbidity, defined as intraventricular haemorrhage grade 3 or 4, or requiring supplemental oxygen at 36 weeks' postmenstrual age, or both. Maternal outcomes were surgery for removal of the placenta, sepsis, admission to an intensive treatment unit, and death. Clinical data included rates of termination of pregnancy for medical reasons. Results Perinatal outcomes were calculated with all terminations of pregnancy for medical reasons excluded, and a worst-best range was calculated assuming that all terminations for medical reasons and those with missing data would have died (minimum value) or all would be liveborn (maximum value). For singleton pregnancies, the live birth rate was 44% (98/223), range 30-62% (98/326-201/326), perinatal survival to discharge from hospital was 26% (54/207), range 17-53% (54/326-173/326), and 18% (38/207), range 12-48% (38/326-157/326) of babies survived without severe morbidity. The rate of maternal sepsis was 12% (39/326) in singleton and 29% (11/38) in multiple pregnancies (P=0.004). Surgery for removal of the placenta was needed in 20% (65/326) and 16% (6/38) of singleton and twin pregnancies, respectively. Five women became severely unwell with sepsis; two died and another three required care in the intensive treatment unit. Conclusions In this study, 26% of women who had very early PPROM with expectant management had babies that survived to discharge from hospital. Morbidity and mortality rates were high for both mothers and neonates. Maternal sepsis is a considerable risk that needs more research. These data should be used in counselling families with PPROM before 23 weeks' gestation, and currently available guidelines should be updated accordingly

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘Omics

The emergence of robust single-cell ‘omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a \u3e 1 Gy old clade). Analysis of the data resulting from these single-cell ‘omics approaches show: 1) the description of the ciliates in the class Karyorelictea as “primitive”is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani’s (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages

The Role of Personality Traits in Young Adult Fruit and Vegetable Consumption

This project investigated how individual differences in the big-five personality traits (neuroticism, extraversion, openness to experience, conscientiousness, and agreeableness) predicted plant-food consumption in young adults. A total of 1073 participants from two samples of young adults aged 17–25 reported their daily servings of fruits, vegetables, and two unhealthy foods for comparison purposes using an Internet daily diary for 21 or 13 days (micro-longitudinal, correlational design). Participants also completed the Neuroticism, Extraversion, Openness Five Factor Inventory (NEO-FFI) measure of personality, and demographic covariates including gender, age, ethnicity, and body mass index (BMI). Analyses used hierarchical regression to predict average daily fruit and vegetable consumption as separate dependent variables from the demographic covariates (step 1) and the five personality traits (step 2). Results showed that young adults higher in openness and extraversion, and to some extent conscientiousness, ate more fruits and vegetables than their less open, less extraverted, and less conscientious peers. Neuroticism and agreeableness were unrelated to fruit and vegetable consumption. These associations were unique to eating fruit and vegetables and mostly did not extend to unhealthy foods tested. Young adult women also ate more fruit and vegetables than young adult men. Results suggest that traits associated with greater intellect, curiosity, and social engagement (openness and extraversion), and to a lesser extent, discipline (conscientiousness) are associated with greater plant-food consumption in this population. Findings reinforce the importance of personality in establishing healthy dietary habits in young adulthood that could translate into better health outcomes later in life

The Design and Validation of the Quantum Mechanics Conceptual Survey

The Quantum Mechanics Conceptual Survey (QMCS) is a 12-question survey of students' conceptual understanding of quantum mechanics. It is intended to be used to measure the relative effectiveness of different instructional methods in modern physics courses. In this paper we describe the design and validation of the survey, a process that included observations of students, a review of previous literature and textbooks and syllabi, faculty and student interviews, and statistical analysis. We also discuss issues in the development of specific questions, which may be useful both for instructors who wish to use the QMCS in their classes and for researchers who wish to conduct further research of student understanding of quantum mechanics. The QMCS has been most thoroughly tested in, and is most appropriate for assessment of (as a posttest only), sophomore-level modern physics courses. We also describe testing with students in junior quantum courses and graduate quantum courses, from which we conclude that the QMCS may be appropriate for assessing junior quantum courses, but is not appropriate for assessing graduate courses. One surprising result of our faculty interviews is a lack of faculty consensus on what topics should be taught in modern physics, which has made designing a test that is valued by a majority of physics faculty more difficult than expected.Comment: Submitted to Physical Review Special Topics: Physics Education Researc

Preliminary Results from a Study Investigating the Transition from Capstone Design to Industry

This study investigates engineering students’ transitions from academic to professional environments by examining the role capstone design courses play in preparing graduates for the workplace. To better understand how capstone design experiences contribute to graduates’ professional preparation, we are collecting data from participants from four different institutions with project-based capstone courses as they begin post-graduation positions in a variety of engineering workplaces. Through quantitative and qualitative methods, our study is designed to collect insights from participants in their first 12 months on the job. Currently we are collecting and analyzing data from the first of two planned cohorts of participants. Preliminary results for the participants in the first cohort point towards interesting trends regarding participants’ frequency of activities and perception of their preparedness. Professional skills such as team meetings were listed most frequently as activities engaged in by participants, and while there were particular areas such as budgeting where participants felt less prepared, overall their perception of preparedness indicates that capstone design courses and the larger engineering curriculum they are housed within are preparing students for professional careers

Activation of STING-Dependent Innate Immune Signaling By S-Phase-Specific DNA Damage in Breast Cancer

Background: Previously we identified a DNA damage response–deficient (DDRD) molecular subtype within breast cancer. A 44-gene assay identifying this subtype was validated as predicting benefit from DNA-damaging chemotherapy. This subtype was defined by interferon signaling. In this study, we address the mechanism of this immune response and its possible clinical significance. Methods: We used immunohistochemistry (IHC) to characterize immune infiltration in 184 breast cancer samples, of which 65 were within the DDRD subtype. Isogenic cell lines, which represent DDRD-positive and -negative, were used to study the effects of chemokine release on peripheral blood mononuclear cell (PBMC) migration and the mechanism of immune signaling activation. Finally, we studied the association between the DDRD subtype and expression of the immune-checkpoint protein PD-L1 as detected by IHC. All statistical tests were two-sided. Results: We found that DDRD breast tumors were associated with CD4+ and CD8+ lymphocytic infiltration (Fisher’s exact test P < .001) and that DDRD cells expressed the chemokines CXCL10 and CCL5 3.5- to 11.9-fold more than DNA damage response–proficient cells (P < .01). Conditioned medium from DDRD cells statistically significantly attracted PBMCs when compared with medium from DNA damage response–proficient cells (P < .05), and this was dependent on CXCL10 and CCL5. DDRD cells demonstrated increased cytosolic DNA and constitutive activation of the viral response cGAS/STING/TBK1/IRF3 pathway. Importantly, this pathway was activated in a cell cycle–specific manner. Finally, we demonstrated that S-phase DNA damage activated expression of PD-L1 in a STING-dependent manner. Conclusions: We propose a novel mechanism of immune infiltration in DDRD tumors, independent of neoantigen production. Activation of this pathway and associated PD-L1 expression may explain the paradoxical lack of T-cell-mediated cytotoxicity observed in DDRD tumors. We provide a rationale for exploration of DDRD in the stratification of patients for immune checkpoint–based therapies

New Engineers’ First Three Months: A Study of the Transition from Capstone Design Courses to Workplaces

In preparing engineering students for the workplace, capstone classes provide unique opportunities for students to develop their professional identities and learn critical skills such as engineering design, teamwork, and self-directed learning (Lutz & Paretti). While existing research explores what and how students learn within these courses, we know much less about how capstone courses affect students’ transitions into the workplace. To address this gap, we are following 62 new graduates from four institutions during the participants’ first 12 weeks of work. Participants were drawn from three mechanical engineering programs and one engineering science program. Women were intentionally oversampled in the study, with 29 participants (47%) identifying as female. Weekly surveys were used to collect quantitative data on what types of workplace activities participants engaged in (e.g., team meetings, project budgeting, CAD modeling, engineering calculations) and qualitative data on what challenges they experience in their early work experience. In this paper, we present a descriptive analysis of the data to identify patterns across participants. Preliminary analysis of the quantitative data suggests that the most common activities for our participants were team meetings and project planning (mentioned by \u3e70% of participants) compared to formal presentations and project budgeting (mentioned by The results are intended to inform both capstone faculty and industry to identify areas of strength and improvement. Our recommendations target current practices in capstone education including course design and structure as well as industry onboarding practices