Engineering bacteria to solve the Burnt Pancake Problem

<p>Abstract</p> <p>Background</p> <p>We investigated the possibility of executing DNA-based computation in living cells by engineering <it>Escherichia coli </it>to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA.</p> <p>Results</p> <p>Inversions (or "flips") of the DNA fragment pancakes are driven by the <it>Salmonella typhimurium </it>Hin/<it>hix </it>DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in <it>E. coli</it>. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; <it>E. coli </it>cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of <it>in vivo </it>flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes.</p> <p>Conclusion</p> <p>The Hin/<it>hix </it>system is a proof-of-concept demonstration of <it>in vivo </it>computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/<it>hix </it>may provide a flexible new tool for manipulating transgenic DNA <it>in vivo</it>.</p

Expectations of and for Clerkship Directors 2.0: A Collaborative Statement from the Alliance for Clinical Education

This article presents an update of the collaborative statement on clerkship directors (CDs), first published in 2003, from the national undergraduate medical education organizations that comprise the Alliance for Clinical Education (ACE). The clerkship director remains an essential leader in the education of medical students on core clinical rotations, and the role of the CD has and continues to evolve. The selection of a CD should be an explicit contract between the CD, their department, and the medical school, with each party fulfilling their obligations to ensure the success of the students, the clerkship and of the CD. Educational innovations and accreditation requirements have evolved in the last two decades and therefore this article updates the 2003 standards for what is expected of a CD and provides guidelines for the resources and support to be provided. In their roles as CDs, medical student educators engage in several critical activities: administration, education/teaching, coaching, advising, and mentoring, faculty development, compliance with accreditation standards, and scholarly activity. This article describes (a) the work products that are the primary responsibility of the CD; (b) the qualifications for the CD; (c) the support structure, resources, and personnel that are necessary for the CD to accomplish their responsibilities; (d) incentives and career development for the CD; and (e) the dedicated time that should be provided for the clerkship and the CD to succeed. Given all that should rightfully be expected of a CD, a minimum of 50% of a full-time equivalent is recognized as appropriate. The complexity and needs of the clerkship now require that at least one full-time clerkship administrator (CA) be a part of the CD’s team. To better reflect the current circumstances, ACE has updated its recommendations for institutions and departments to have clear standards for what is expected of the director of a clinical clerkship and have correspondingly clear guidelines as to what should be expected for CDs in the support they are provided. This work has been endorsed by each of the eight ACE member organizations

Remission Of Maternal Depression And Child Symptoms Among Single Mothers: A Star*d-child Report

Objective: Offspring of depressed parents are at increased risk for depressive and other disorders. We recently found that when depressed mothers reached full remission over 3 months of treatment, a significant improvement in the children’s disorders occurred. Since only a third of the mothers remitted, factors related to maternal remission rates, and thereby child outcomes, were important. This report examined the relationship of the presence of a father in the household to maternal depression remission and child outcomes. Method: Maternal depression was measured using the 17-item Hamilton Rating Scale for Depression (HRSD17); social functioning was assessed using the Social Adjustment Scale-Self Report (SAS-SR). Children (age 7–17) were assessed independently, blind to maternal outcome, using the Schedule for Affective Disorders and Schizophrenia for School-Age Children (K-SADS-PL) and the Child Global Assessment Scale (C-GAS). Results: Single mothers (n = 50), as compared to those in two-parent households (n = 61), were more likely to discontinue treatment (31% vs. 16%, P = 0.04), and less likely to remit if they remained in treatment (20% vs. 43%, P = 0.013). These differences remained significant after adjusting for socioeconomic status and potential confounders, but were partially explained by the mother’s pre-treatment social functioning. The reduction in child diagnoses following maternal remission was greater in two-parent than in single-parent households, although a formal test of interaction between the odds ratios was not significant. Conclusion: Single depressed mothers are more likely to drop out of treatment, and less likely to reach remission if they stay in treatment. This high-risk group requires vigorous treatment approaches

Place-Based Learning Communities on a Rural Campus: Turning Challenges into Assets

At Humboldt State University (HSU), location is everything. Students are as drawn to our spectacular natural setting as they are to the unique majors in the natural resource sciences that the university has to offer. However, the isolation that nurtures the pristine natural beauty of the area presents a difficult reality for students who are accustomed to more densely populated environments. With the large majority of our incoming students coming from distant cities, we set out to cultivate a “home away from home” by connecting first-year students majoring in science, technology, engineering and math (STEM) to the communities and local environment of Humboldt County. To achieve this, we designed first-year place-based learning communities (PBLCs) that integrate unique aspects and interdisciplinary themes of our location throughout multiple high impact practices, including a summer experience, blocked-enrolled courses, and a first-year experience course entitled Science 100: Becoming a STEM Professional in the 21st Century. Native American culture, traditional ways of knowing, and contemporary issues faced by tribal communities are central features of our place-based curriculum because HSU is located on the ancestral land of the Wiyot people and the university services nine federally recognized American Indian tribes. Our intention is that by providing a cross-cultural, validating environment, students will: feel and be better supported in their academic pursuits; cultivate values of personal, professional and social responsibility; and increase the likelihood that they will complete their HSU degree. As we complete the fourth year of implementation, we aim to harness our experience and reflection to improve our programming and enable promising early results to be sustained

Course and Severity of Maternal Depression: Associations with Family Functioning and Child Adjustment

Number of lifetime episodes, duration of current episode, and severity of maternal depression were investigated in relation to family functioning and child adjustment. Participants were the 151 mother–child pairs in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) child multi-site study. Mothers were diagnosed with Major Depressive Disorder; children (80 males and 71 females) ranged in age from 7 to 17 years. Measures of child adjustment included psychiatric diagnoses, internalizing and externalizing symptoms, and functional impairment. Measures of family functioning included family cohesion, expressiveness, conflict, organization, and household control; parenting measures assessed maternal acceptance and psychological control. Children of mothers with longer current depressive episodes were more likely to have internalizing and externalizing symptoms, with this association being moderated by child gender. Mothers with more lifetime depressive episodes were less likely to use appropriate control in their homes

Remission of Maternal Depression: Relations to Family Functioning and Youth Internalizing and Externalizing Symptoms

Family functioning and parenting were hypothesized to mediate the relation between remission of maternal depression and children's psychosocial adjustment. Participants were 114 mother-child dyads participating in the Sequenced Treatment Alternatives to Relieve Depression Child 3-month follow-up. All mothers had been diagnosed with major depressive disorder and were treated initially with citalopram; 33% of mothers experienced remission of depressive symptoms. Youth ranged in age from 7 to 17. Remission of maternal depression was associated with changes in children's reports of their mothers' warmth/acceptance, which in turn partially mediated the relation between maternal depression remission and youth internalizing symptoms, accounting for 22.9% of the variance

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building

Brain multiplexes reveal morphological connectional biomarkers fingerprinting late brain dementia states

Accurate diagnosis of mild cognitive impairment (MCI) before conversion to Alzheimer’s disease (AD) is invaluable for patient treatment. Many works showed that MCI and AD affect functional and structural connections between brain regions as well as the shape of cortical regions. However, ‘shape connections’ between brain regions are rarely investigated -e.g., how morphological attributes such as cortical thickness and sulcal depth of a specific brain region change in relation to morphological attributes in other regions. To fill this gap, we unprecedentedly design morphological brain multiplexes for late MCI/AD classification. Specifically, we use structural T1-w MRI to define morphological brain networks, each quantifying similarity in morphology between different cortical regions for a specific cortical attribute. Then, we define a brain multiplex where each intra-layer represents the morphological connectivity network of a specific cortical attribute, and each inter-layer encodes the similarity between two consecutive intra-layers. A significant performance gain is achieved when using the multiplex architecture in comparison to other conventional network analysis architectures. We also leverage this architecture to discover morphological connectional biomarkers fingerprinting the difference between late MCI and AD stages, which included the right entorhinal cortex and right caudal middle frontal gyrus