Understanding 'error' in the forensic sciences: A primer.

This paper distils seven key lessons about 'error' from a collaborative webinar series between practitioners at Victoria Police Forensic Services Department and academics. It aims to provide the common understanding of error necessary to foster interdisciplinary dialogue, collaboration and research. The lessons underscore the inevitability, complexity and subjectivity of error, as well as opportunities for learning and growth. Ultimately, we argue that error can be a potent tool for continuous improvement and accountability, enhancing the reliability of forensic sciences and public trust. It is hoped the shared understanding provided by this paper will support future initiatives and funding for collaborative developments in this vital domain.

Chondrocyte-to-osteoblast transformation in mandibular fracture repair.

The majority of fracture research has been conducted using long bone fracture models, with significantly less research into the mechanisms driving craniofacial repair. However, craniofacial bones differ from long bones in both their developmental mechanism and embryonic origin. Thus, it is possible that their healing mechanisms could differ. In this study we utilize stabilized and unstabilized mandible fracture models to investigate the pathways regulating repair. Whereas fully stable trephine defects in the ramus form bone directly, mechanical motion within a transverse fracture across the same anatomical location promoted robust cartilage formation before boney remodeling. Literature investigating long bone fractures show chondrocytes are a direct precursor of osteoblasts during endochondral repair. Lineage tracing with Aggrecan-CreERT2 ::Ai9 tdTomato mice demonstrated that mandibular callus chondrocytes also directly contribute to the formation of new bone. Furthermore, immunohistochemistry revealed that chondrocytes located at the chondro-osseous junction expressed Sox2, suggesting that plasticity of these chondrocytes may facilitate this chondrocyte-to-osteoblast transformation. Based on the direct role chondrocytes play in bone repair, we tested the efficacy of cartilage grafts in healing critical-sized mandibular defects. Whereas empty defects remained unbridged and filled with fibrous tissue, cartilage engraftment produced bony-bridging and robust marrow cavity formation, indicating healthy vascularization of the newly formed bone. Engrafted cartilage directly contributed to new bone formation since a significant portion of the newly formed bone was graft/donor-derived. Taken together these data demonstrate the important role of chondrocyte-to-osteoblast transformation during mandibular endochondral repair and the therapeutic promise of using cartilage as a tissue graft to heal craniofacial defects.

Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding.

Two common features of centromeres are their transcription into noncoding centromere RNAs (cen-RNAs) and their assembly into nucleosomes that contain a centromere-specific histone H3 (cenH3). Here, we show that Saccharomyces cerevisiae cen-RNA was present in low amounts in wild-type (WT) cells, and that its appearance was tightly cell cycle-regulated, appearing and disappearing in a narrow window in S phase after centromere replication. In cells lacking Cbf1, a centromere-binding protein, cen-RNA was 5-12 times more abundant throughout the cell cycle. In WT cells, cen-RNA appearance occurred at the same time as loss of Cbf1's centromere binding, arguing that the physical presence of Cbf1 inhibits cen-RNA production. Binding of the Pif1 DNA helicase, which happens in mid-late S phase, occurred at about the same time as Cbf1 loss from the centromere, suggesting that Pif1 may facilitate this loss by its known ability to displace proteins from DNA. Cen-RNAs were more abundant in rnh1Δ cells but only in mid-late S phase. However, fork pausing at centromeres was not elevated in rnh1Δ cells but rather was due to centromere-binding proteins, including Cbf1 Strains with increased cen-RNA lost centromere plasmids at elevated rates. In cbf1Δ cells, where both the levels and the cell cycle-regulated appearance of cen-RNA were disrupted, the timing and levels of cenH3 centromere binding were perturbed. Thus, cen-RNAs are highly regulated, and disruption of this regulation correlates with changes in centromere structure and function.

Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range.

Genetically encoded Förster resonance energy transfer (FRET) sensors enable the visualization of ions, molecules, and processes in live cells. However, despite their widespread use, the molecular states that determine sensor performance are usually poorly understood, which limits efforts to improve them. We used dynamic light scattering (DLS) and time-resolved fluorescence anisotropy to uncover the sensing mechanism of ZifCV1.173, a Zn2+ FRET sensor. We found that the dynamic range (DR) of ZifCV1.173 was dominated by the high FRET efficiency of the Zn2+-free state, in which the donor and acceptor fluorescent proteins were closely associated. Mutating the donor-acceptor interface revealed that the DR of ZifCV1.173 could be increased or decreased by promoting or disrupting the donor-acceptor interaction, respectively. Adapting the same mutations to a related sensor showed the same pattern of DR tuning, supporting our sensing mechanism and suggesting that DLS and time-resolved fluorescence anisotropy might be generally useful in the biophysical characterization of other FRET sensors.

Increased litigation burden among tibia, pelvis, and spine fractures: An analysis of 756 fracture-related malpractice cases.

OBJECTIVES: To analyze a series of claims from a large national malpractice insurer associated with fracture care to understand what parameters are associated with claims, defense costs, and paid indemnity. DESIGN: Review of claims in fracture care settings from a national database; case series. SETTING: Database draws from insured pool of 400,000 medical malpractice cases from 400 healthcare entities across the country, representing 165,000 physicians; both academic and private. PATIENTS/PARTICIPANTS: Fracture care patients bringing legal suit. MAIN OUTCOME MEASUREMENTS: Cost of legal proceedings and indemnity, ICD-9 codes, and contributing causes toward claims. RESULTS: A total of 756 fracture claims were asserted between 2005 and 2014 regarding fracture care within the database; 70% were brought for inaccurate, missed, or delayed diagnosis, while 22% addressed medical treatment and 8% were for surgical management. Orthopaedics was the primary service in 22%. Total cost (expenses and indemnity) to orthopaedic providers totaled $13.1MM (million). The most common claim against orthopaedics was for fractures of the tibia and fibula (11.4%). Impact factor (IF) analysis (as described by Matsen) of indemnity in these cases reveals 3 fracture regions of highest indemnity burden: fractures of the tibia and fibula (IF: 1.86, 11.4%), pelvis (IF: 1.77, 6.6%), and spine (IF 1.33, 6.6%). Analysis of contributing factors identifies the category of clinical judgement as the most common category (62%). Other common factors include patient noncompliance (31%), communication (28%), technical skill (17%), clinical systems (11%), and documentation (10%). The single most common specific cause of a claim in orthopaedic fracture care was misinterpretation of diagnostic imaging (25%). CONCLUSION: This study is the first of its kind to identify fractures of the tibia and fibula as high risk for litigation against orthopaedic providers and provides general counseling of legal pitfalls in fracture care. Finally, we are able to identify the act of patient assessment as a key issue in over half of all fracture-related claims against orthopaedic providers. Providers in general and specialty settings can use this information to help guide their treatment and care ownership decisions in the care of patients with fractures. LEVEL OF EVIDENCE: Economic - Level III.

Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure.

Vibrational spectroscopy is a powerful tool for characterizing the complex noncovalent interactions that arise in biological systems. The nitrile stretching frequency has proven to be a particularly convenient biological probe, but the interpretation of nitrile spectroscopy is complicated by its sensitivity to local hydrogen bonding interactions. This often inhibits the straightforward interpretation of nitrile spectra by requiring knowledge of the molecular-level details of the local environment surrounding the probe. While the effect of hydrogen bonds on nitrile frequencies has been well-documented for small molecules in solution, there have been relatively few studies of these effects in a complex protein system. To address this, we introduced a nitrile probe at nine locations throughout green fluorescent protein (GFP) and compared the mean vibrational frequency of each probe to the specific hydrogen bonding geometries observed in molecular dynamics (MD) simulations. We show that a continuum of hydrogen bonding angles is found depending on the particular location of each nitrile, and that the differences in these angles account for the differences in the measured nitrile frequency. We further observed that the temperature dependence of the nitrile frequencies (measured as a frequency-temperature line slope, FTLS) was a good indicator of the hydrogen bonding interactions of the probe, even in scenarios where the nitrile was involved in complex and restricted hydrogen bonds, both from protein and from water. While constant offsets to the nitrile frequency to all hydrogen bonding environments have been applied before to interpret shifts in nitrile frequency, we show that this is insufficient in systems where the hydrogen bonds may be restricted by the surrounding medium. However, the strength of the observed correlation between nitrile frequency and hydrogen bonding angle suggests that it may be possible to disentangle electrostatic effects and effects of the orientation of hydrogen bonding on the nitrile stretching frequency. Meanwhile, the experimental measurement of the FTLS of the nitrile is an excellent tool to identify changes in the hydrogen bonding interactions for a particular probe.

Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes.

Measurement of the electrostatic interactions that give rise to biological functions has been a longstanding challenge in biophysics. Advances in spectroscopic techniques over the past two decades have allowed for the direct measurement of electric fields in a wide variety of biological molecules and systems via the vibrational Stark effect (VSE). The frequency of the nitrile stretching oscillation has received much attention as an electric field reporter because of its sensitivity to electric fields and its occurrence in a relatively transparent region of the infrared spectrum. Despite these advantages and its wide use as a VSE probe, the nitrile stretching frequency is sensitive to hydrogen bonding in a way that complicates the straightforward relationship between measured frequency and environmental electric field. Here we highlight recent applications of nitrile VSE probes with an emphasis on experiments that have helped shape our understanding of the determinants of nitrile frequencies in both hydrogen bonding and nonhydrogen bonding environments.

A Double Decarboxylation in Superfolder Green Fluorescent Protein Leads to High Contrast Photoactivation.

A photoactivatable variant of superfolder green fluorescent protein (GFP) was created by replacing the threonine at position 203 with aspartic acid. Photoactivation by exposure of this mutant to UV light resulted in conversion of the fluorophore from the neutral to the negatively charged form, accompanied by a ∼95-fold increase in fluorescence under 488 nm excitation. Mass spectrometry before and after exposure to UV light revealed a change in mass of 88 Da, attributed to the double decarboxylation of Glu 222 and Asp 203. Kinetics studies and nonlinear power-dependence of the initial rate of photoconversion indicated that the double decarboxylation occurred via a multiphoton absorption process at 254 nm. In addition to providing a photoactivatable GFP with robust folding properties, a detailed mechanistic understanding of this double decarboxylation in GFP will lead to a better understanding of charge transfer in fluorescent proteins.

Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pKa Shifts Provide a Unique Benchmark for Electrostatics Models.

Measurement of the magnitude, direction, and functional importance of electric fields in biomolecules has been a long-standing experimental challenge. pKa shifts of titratable residues have been the most widely implemented measurements of the local electrostatic environment around the labile proton, and experimental data sets of pKa shifts in a variety of systems have been used to test and refine computational prediction capabilities of protein electrostatic fields. A more direct and increasingly popular technique to measure electric fields in proteins is Stark effect spectroscopy, where the change in absorption energy of a chromophore relative to a reference state is related to the change in electric field felt by the chromophore. While there are merits to both of these methods and they are both reporters of local electrostatic environment, they are fundamentally different measurements, and to our knowledge there has been no direct comparison of these two approaches in a single protein. We have recently demonstrated that green fluorescent protein (GFP) is an ideal model system for measuring changes in electric fields in a protein interior caused by amino acid mutations using both electronic and vibrational Stark effect chromophores. Here we report the changes in pKa of the GFP fluorophore in response to the same mutations and show that they are in excellent agreement with Stark effect measurements. This agreement in the results of orthogonal experiments reinforces our confidence in the experimental results of both Stark effect and pKa measurements and provides an excellent target data set to benchmark diverse protein electrostatics calculations. We used this experimental data set to test the pKa prediction ability of the adaptive Poisson-Boltzmann solver (APBS) and found that a simple continuum dielectric model of the GFP interior is insufficient to accurately capture the measured pKa and Stark effect shifts. We discuss some of the limitations of this continuum-based model in this system and offer this experimentally self-consistent data set as a target benchmark for electrostatics models, which could allow for a more rigorous test of pKa prediction techniques due to the unique environment of the water-filled GFP barrel compared to traditional globular proteins.

Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding.

There is growing interest in using the nitrile vibrational oscillation as a site-specific probe of local environment to study dynamics, folding, and electrostatics in biological molecules such as proteins. Nitrile probes have been used extensively as reporters of electric field using vibrational Stark effect spectroscopy. However, the analysis of frequencies in terms of electric fields is potentially complicated by the large ground state dipole moment of the nitrile, which may irrevocably perturb the protein under investigation, and the ability of nitriles to accept hydrogen bonds, which causes frequency shifts that are not described by the Stark effect. The consequence of this is that vibrational spectroscopy of nitriles in biomolecules could be predominately sensitive to their local hydration status, not electrostatic environment, and have the potential to be particularly destabilizing to the protein. Here, we introduce green fluorescent protein (GFP) as a model system for addressing these concerns using biosynthetically incorporated p-cyanophenylalanine (pCNF) residues in the interior of GFP and measuring absorption energies of both the intrinsic GFP fluorophore and pCNF residues in response to a series of amino acid mutations. We show that observed changes in emission energy of GFP due to the mutations strongly correlate with changes in electric field experienced by both the nitrile probes and the intrinsic fluorophore. Additionally, we show that changes in electric field measured from the intrinsic fluorophore due to amino acid mutations are unperturbed by the addition of pCNF residues inserted nearby. Finally, we show that changes in electric field experienced by the vibrational probes trend monotonically with changes in field experienced by the native fluorophore even though the nitrile probe is engaged in moderate hydrogen bonding to nearby water molecules, indicated by the temperature dependence of the nitrile's absorption energy. Together these results demonstrate that even in the presence of hydrogen bonding it is possible to relate nitrile absorption frequencies to electrostatic environment by comparing highly similar environments. GFP's intrinsic linear sensitivity to electric fields makes it a convenient model system for studying electrostatics in proteins that offers lessons for proteins without this visible fluorophore.