The accurate and precise measurement of endogenous steroid hormone levels in serum is essential for their use as biomarkers of endocrine and metabolic diseases in patient care and translational science. Herein, we describe a newly developed, highly accurate, and precise isotope-dilution liquid chromatography-mass spectrometry (LC-MS/MS) method capable of simultaneously measuring eight clinically relevant polar and non-polar steroid hormones in 200 µL of serum. This steroid hormone panel method uses sequential liquid-liquid extractions for the isolation of total testosterone (TT), estradiol (E2), progesterone (P4), 17-hydroxyprogesterone (17-OHP), androstenedione (AD), estrone (E1), estrone sulfate (E1S), and dehydroepiandrosterone sulfate (DHEAS) without derivatization or hydrolysis. The method demonstrated a broad analytical measurement range for all eight hormones as a result of improved selectivity and sensitivity, making it suitable for the analysis of general population serum samples, including postmenopausal women and children. The total imprecision, expressed as coefficients of variation, was evaluated at three levels for each analyte and ranged from 3.5 to 10.7
Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.
Screening of nucleic acid synthesis orders is expanding to include short, single-stranded DNA orders in efforts to ensure potentially harmful genes and genomes cannot be synthesized by illegitimate or irresponsible customers. Short sequence fragments are not as information rich as gene sequences, typically require assembly to be functional, and are much cheaper to produce than genes. Thus, here we provide the perspective that the screening of sequence fragments requires a different approach than sequence-by-sequence screening by considering the context of other fragments in the order or across orders. Additional and alternative metrics should be included while screening fragments, such as fraction of the gene/genome covered and evidence of potential use for assembly to enable efficient and accurate biosecurity screening. We further demonstrate two existing biosecurity tools, UltraQUICK and Aclid that provide outputs for better understanding the threat of orders containing fragments. This perspective provides a foundation for how short DNA fragments, including oligo pools, should be screened and leaves the reader with considerations for overall risk assessments of such orders based on the functional and taxonomic characteristics of the order.
Abstract With shifting environmental trends, many Earth system elements may be poised to undergo critical transitions or ‘tipping’. Reliable anticipation of these tipping elements is vital to inform policy decisions. Many of the current methods for tipping point detection are based on loss of resilience or ‘critical slowdown’ of the system as it approaches a tipping point. However, these methods are prone to false alarms; the detected slowdown may be an artifact of nonstationary noise unrelated to tipping behavior. Here, we explore the efficacy of early warning signs based on a nonequilibrium thermodynamics framework. The model-free detection method relies on the increased intrinsic time-irreversibility due to detailed balance breaking, preceding the onset of tipping or instabilities. We demonstrate that these EWSs are effective for tipping point detection and robust against false alarms due to nonstationary noise, using idealized models for two key elements of the Earth system that are prone to tipping: the Atlantic Meridional Overturning Circulation and Arctic sea-ice loss.
Readily available nucleic acid synthesis is both critical for the bioeconomy and an increasingly pressing security concern due to the potential for accidental or deliberate misuse. While biosecurity experts broadly agree that nucleic acid providers should screen orders for potential “sequences of concern,” there has previously been no agreed standard for how to define and recognize such sequences. To address this gap, we first organized a collection of test sets containing 1.1 million sequences from pathogens and toxins on the Australia Group Common Control Lists and their non-controlled relatives, along with model organisms and synthetic constructs. An initial categorization of sequences as to whether or not they were sequences of concern was produced by comparing the results of four biosecurity screening systems for each of these sequences, finding that these systems already agreed on the categorization of more than 80% of sequences. We then refined these results through a science-based stakeholder review process to define a rubric for determining whether a sequence should be flagged as a potential sequence of concern, then applied this rubric to improve the categorization of sequences in test sets. The result is a rubric that identifies sequences of concern with respect to human pandemic-potential viruses, key classes of low-risk genes, and controlled toxins. Applying this rubric to the test set collection has, to date, reduced the number of test sequences with disputed categorization by 44.3% for controlled viruses and 10.7% across the collection of test sets as a whole. Together, the rubric and the test sets provide a concrete “sequence of concern” definition that can be used as a foundation for development of biosecurity screening standards and policy and is also continuing to be refined in ongoing work.
