Assessing human exposure to emerging contaminants using high-resolution MS

Department of Aquatic Sciences and Assessment Third-cycle subject area Biology Description of the doctoral project   Antimicrobial resistance (AMR) is one of the most pressing global health challenges of our time. A key driver of AMR spread is the horizontal transfer of antibiotic resistance genes via conjugative plasmids — mobile genetic elements that move between bacteria. Plasmid-dependent phages (PDPs) are viruses that specifically infect bacteria carrying these plasmids, making them a potentially powerful but largely overlooked tool in controlling resistance gene transmission. This PhD project is part of ECOPHARM, a research project funded by the Knut and Alice Wallenberg Foundation (Wallenberg Academy Fellows 2025) and is based at the Department of Aquatic Sciences and Assessment, SLU Uppsala. The overarching aim of ECOPHARM is to decipher the mechanisms driving PDP interactions with conjugative plasmids and bacterial hosts, and to understand their impact on antibiotic resistance gene transmission in aquatic environments. As a PhD student, you will investigate the diversity, ecology, and functional interactions of plasmid-dependent phages in aquatic ecosystems. The work will combine environmental sampling, cultivation-based approaches, metagenomics, genome analysis, and experimental infection assays. You will work in a dynamic and internationally connected research environment at the intersection of microbial ecology, virus-host coevolution, and AMR research. To learn more about our research you can check out our webpage https://www.bionomics-mmlab.com/ About the position The PhD student will be expected to: Design and carry out field sampling of aquatic environments to characterize PDP communities Perform laboratory experiments to study PDP–plasmid–host interactions under controlled conditions Apply metagenomic and bioinformatic tools to analyze microbial and viral community data Contribute to experimental work on phage isolation, cultivation, and infection assays Present findings at lab meetings, national and international conferences, and contribute to scientific publications Adhere to lab policies on data management practices Communicate progress and bottlenecks timely and clearly Collaborate with national and international project partners within the ECOPHARM network Requirements To meet the general entry requirements you must have been awarded a second-cycle (Master's) qualification, satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle, or acquired substantially equivalent knowledge in some other way in Sweden or abroad (Higher Education Ordinance 1993:100, Chapter 7, Section 39). Specific entry requirements for the third-cycle courses and study programme in biology. To meet the specific entry requirements, you must have at least 90 HEC in biology-related subjects. This must include a degree project and at least 30 HEC must be at second-cycle level. You must also meet the equivalent English language requirements as those necessary for the Swedish upper-secondary qualification Engelska B/6. Your profile Required: A Master's degree in microbiology, biology, molecular biology, environmental science, or a closely related field Solid background in microbiology or molecular biology Experience with laboratory techniques relevant to microbial or environmental research Proficiency in written and spoken English Highly desirable: Experience with bioinformatics or computational analysis of sequencing data Familiarity with phage biology, plasmid biology, or antimicrobial resistance research Experience with aquatic or environmental sampling Personal qualities we are looking for: High agency — you take initiative, define problems independently, and push work forward engaging your supervisor Collaborative mindset — you contribute actively to a team environment and support those around you Clear communicator — you can convey complex ideas in writing and in person, to both specialist and non-specialist audiences Curiosity, rigor, and resilience in the face of scientific uncertainty About us The Department of Aquatic Sciences and Assessment is working with applied environmental science, with a national responsibility for assessing the condition of Swedish surface waters with respect to water chemistry, pollution and aquatic biota. The research focuses on geochemical and hydrological processes, aquatic ecology and biodiversity, microbial ecology as well as on environmental chemistry and aquatic ecotoxicology. The department has about 150 employees, of which approximately half are researchers/doctoral students and the other half are technical and administrative staff. For more information about the department visit: http://www.slu.se/aquatic-sciences Read more about staff benefits and life as an SLU employee on https://www.slu.se/om-slu/jobba-pa-slu/ Read more about third-cycle courses and study programmes on http://www.slu.se/utbildning/program-kurser/forskarutbildning/ Form of employment / Funding Employment as a doctoral student (4-year programme) Doctoral student's salaries are set following the local collective agreement. Salary progression is fixed. Location: Uppsala Scope: 100% Start date: 1st of October 2026 Application and selection: Please submit your application using the link below. The deadline is 30th of August 2026. Your application should include: A one-page reflection including (1) why you plan to pursue a PhD education (2) why specifically you think our group is a good target for you and (3) why this project interests you Send 2 publications related to the topic of "plasmid dependent phages" that you find most interesting All application documents should be prepared in English Read more about the other attachments that your application should include at https://www.slu.se/en/study/programmes-courses/doctoral-education/how-can-i-become-a-doctoral-student/application/ Selection among eligible applicants is based on the documents attached to the application, and is carried out with regard to the applicant's ability to complete the programme within the allotted time. Academic union representatives: https://internt.slu.se/en/my-employment/employee-associations/kontaktpersoner-vid-rekrytering/

Department overview: The Front Office AI Technology Team sits within the Front Office Technology department and provides a shared capability for the development, operation, and adoption of AI across the firm. The team is responsible for building and supporting enterprise‑grade AI capabilities, including LLM‑powered applications, retrieval‑augmented generation (RAG) systems, agent‑assisted workflows, and scalable internal AI tooling. We develop the core AI foundations required to deploy AI safely and at scale, while also working closely with the business to ensure these capabilities are used effectively in day‑to‑day workflows. This includes supporting experimentation, guiding practical adoption, and helping teams embed AI into real processes where it delivers measurable benefit. A key focus of The Front Office AI Technology Team is ensuring that AI solutions are reliable, secure, and aligned with the firm’s control and risk frameworks. The team balances innovation with discipline, providing common tooling, patterns, and guidance that allow AI to be used consistently and responsibly across research and operational contexts. Role overview: Key Responsibilities: AI Enablement & Integration * Act as a go‑to point of contact for teams who want to understand what AI tools are available and how to use them effectively. * Run workshops, demos, and hands‑on sessions that help users understand the benefit of using LLMs and emerging AI related technologies both for business users and more technical teams. * Support day‑to‑day adoption of Microsoft Copilot, ChatGPT and Claude alongside other approved AI tools by embedding them into real workflows. Training & Best Practice * Deliver practical training on prompt engineering, AI limitations, and good usage patterns for both technical and non‑technical audiences. * Create and maintain reusable materials such as prompt examples/libraries, walkthroughs, and short guidance notes. * Continuously refine training content based on user feedback and emerging best practice. Understanding Business Processes * Spend time with teams to understand their existing processes, pain points, and where work is slow, repetitive, or manual. * Help teams articulate problems clearly enough that AI tooling can be applied sensibly. * Map simple end‑to‑end workflows and identify realistic opportunities for AI assistance. Light Prototyping & Applied AI * Build simple prototypes or proof‑of‑concept workflows using Python, internal libraries, or approved AI APIs alongside tools such as MS Copilot Studio. * Pair with engineers or platform teams when ideas move beyond quick prototypes. * Focus on small, shippable improvements rather than large, speculative solutions. Feedback & Continuous Improvement * Collect structured feedback on what works, what doesn’t, and where users get stuck. * Share insights with The Front Office AI Tech Team, governance, and Infrastructure Tech teams to help guide tooling, documentation, and prioritisation. * Help surface recurring themes rather than one‑off requests. Adoption Metrics, Reporting & Insight * Support the definition and tracking of adoption metrics for approved internal AI tools. * Work with Front Office Technology and platform teams to help maintain simple reporting and dashboards that show usage and engagement patterns (for example: active users, frequency of use, and common use cases). * Monitor adoption trends and identify areas of low engagement or friction that may require additional enablement, training, or tooling changes. * Combine quantitative usage data with qualitative user feedback to build a clear view of how AI tools are being used in practice. * Share regular adoption insights with relevant stakeholders to inform prioritisation of training materials, documentation, and incremental improvements to AI tooling. Why this role exists: The firm is investing heavily in modern AI platforms and tools, but technology alone does not create value. Real impact comes when teams change how they work. This role exists to help front‑office and technology teams translate AI capability into everyday practice, replacing one‑off experimentation with well‑understood patterns, better habits, and repeatable workflows. Through hands‑on enablement, training, and applied problem‑solving, the AI Integration Lead ensures that AI use is both effective and appropriately governed, allowing teams to move faster without increasing operational or compliance risk. What makes this role different: This role offers the chance to work directly with trading desks, providing a rare and exciting opportunity to gain direct front-office exposure. You’ll work at the intersection of business context and applied AI: understanding how teams operate, then helping them adopt approved AI tools safely and effectively through training, workflow mapping, and lightweight prototyping. It’s ideal for someone who enjoys ambiguity, values practical impact over hype, and wants to see their work change how teams operate day-to-day.   Skills & Experience Essential: * Demonstrated interest in evolving applied AI technologies and their use in improving real business processes in a practical and controlled manner. * Experience delivering or supporting training, workshops, or enablement sessions for technical and non‑technical audiences. * Hands‑on experience using modern AI tools beyond typical end‑user interaction, including:                 - Practical understanding of prompt engineering techniques and common LLM failure modes                 - Experience grounding AI outputs in data (e.g. through document retrieval, APIs, MCP or structured context rather than free‑text prompting alone)                 - Exposure to designing AI‑assisted workflows that support repeatable tasks rather than one‑off interactions. * Familiarity with enterprise and low‑code AI tooling, such as Microsoft Power Apps, Power Automate, Copilot Studio, Claude Cowork, or similar workflow and AI enablement platforms. * Practical experience assessing AI output quality and limitations for real business use cases, and iterating prompts or workflows to improve reliability. * Comfortable working with Python at a practical level (scripts, APIs, data handling), without requiring production‑grade engineering expertise. * Strong communication skills, with the ability to explain technical concepts clearly to non‑technical users. * Comfortable operating in environments with evolving requirements, and able to iterate pragmatically rather than waiting for complete specifications. Desirable: * Familiarity with retrieval‑augmented generation (RAG) concepts at a practical level, such as working with internal documents or structured reference data. * Experience designing or supporting simple AI‑assisted workflows for document handling, summarisation, data extraction, or knowledge access. * Awareness of responsible AI considerations in regulated environments, including basic data handling, validation of outputs, and appropriate human review. * Exposure to lightweight agent‑style patterns (e.g. tool use, structured outputs, task decomposition), without requiring ownership of complex agent frameworks. About you: You are a bright and approachable individual who works well with others and enjoys understanding how different teams operate in practice. You are comfortable engaging with both technical and non‑technical stakeholders and are able to communicate clearly and pragmatically. Alongside your technical experience, you may bring experience from a client‑facing or commercially oriented role earlier in your career, which helps you understand business priorities and frame solutions in a way that resonates with users. You have a strong interest in applied AI and a genuine curiosity about how emerging tools can improve the way people work. You are motivated to explore new capabilities, experiment hands‑on, and understand where AI can add value in real workflows. Your approach is practical rather than theoretical, and you are focused on achievable improvements rather than technology for its own sake. You take a considered and responsible approach to AI integration. You are aware of the limitations of AI tools and the importance of appropriate controls, validation, and oversight, particularly in a regulated environment. You are comfortable discussing both the benefits and constraints of AI with users, helping set realistic expectations and encouraging sensible use. You work well in collaborative environments where priorities and requirements evolve. You are adaptable, open to feedback, and comfortable learning by doing. You take satisfaction from helping others build confidence with new tools and from supporting inte across teams, bringing a constructive and measured mindset to your work.   BlueCrest is committed to providing an inclusive environment for its workforce. As an employer, we provide equal opportunities to all people regardless of their gender, marital or civil partnership status, race, religion or ethnicity, disability, age, sexual orientation or nationality.