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Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype–phenotype relationships 1 , 2 . Here we present a human ‘all-by-all’ reference interactome map of human binary protein interactions, or ‘HuRI’. With approximately 53,000 protein–protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome 3 , transcriptome 4 and proteome 5 data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein–protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes. A human binary protein interactome map that includes around 53,000 protein–protein interactions involving more than 8,000 proteins provides a reference for the study of human cellular function in health and disease.

Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq's improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination.

In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical‐versus‐functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an “inter‐interactome” approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter‐interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra‐species networks. Although substantially reduced relative to intra‐species networks, the levels of functional overlap in the yeast–human inter‐interactome network uncover significant remnants of co‐functionality widely preserved in the two proteomes beyond human–yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co‐functionality. Such non‐functional interactions, however, represent a reservoir from which nascent functional interactions may arise. Synopsis An inter‐species “inter‐interactome” was generated by systematic mapping protein–protein interactions between human and yeast proteomes. Comparisons of the inter‐species interactome with the two “parent” intra‐species human and yeast networks reveal evolutionary constraints and plasticity of biological systems. The human and yeast proteomes widely retain the ability to form inter‐species protein–protein interactions. Inter‐species interactions significantly but not exclusively correspond to ancestral binding properties preserved in human and yeast proteins. Ancestral binding properties appear to underlie conserved and species‐specific functions. Graphical Abstract An inter‐species “inter‐interactome” was generated by systematic mapping protein–protein interactions between human and yeast proteomes. Comparisons of the inter‐species interactome with the two “parent” intra‐species human and yeast networks reveal evolutionary constraints and plasticity of biological systems.

A sequence-verified collection of human transcription factors is reported. The authors used it in the enhanced yeast-one hybrid (eY1H) assay to map human gene regulatory networks. Also in this issue, Reece-Hoyes et al . describe the eY1H pipeline. Gateway-compatible yeast one-hybrid (Y1H) assays provide a convenient gene-centered (DNA to protein) approach to identify transcription factors that can bind a DNA sequence of interest. We present Y1H resources, including clones for 988 of 1,434 (69%) predicted human transcription factors, that can be used to detect both known and new interactions between human DNA regions and transcription factors.

Walking is an important skill with positive impacts on health, function, and well-being. Many disorders impair walking and its positive impacts through a variety of complex and interrelated mechanisms. Any attempt to understand walking impairments, or the effects of interventions intended to treat these impairments, must respect this complexity. Therefore, our main objectives in conducting this study were to (1) propose a comprehensive model for quantifying the causes and consequences of walking impairments and (2) demonstrate the potential utility of the model for supporting clinical care and addressing basic scientific questions related to walking. To achieve these goals, we introduced a model, described by a directed acyclic graph, consisting of 10 nodes and 23 primary causal paths. We gave detailed descriptions of each node and path based on domain knowledge. We then demonstrated the model’s utility using a large sample of gait data (N = 9504) acquired as part of routine care at a regional referral center. We analyzed five relevant examples that involved many of the model’s nodes and paths. We computed causal effect magnitudes as Shapley values and displayed the overall importance of variables (mean absolute Shapley value), the variation of Shapley values with respect to underlying variables, and Shapley values for individual observations (case studies). We showed that the model was plausible, captured some well-known cause-effect relationships, provided new insights into others, and generated novel hypotheses requiring further testing through simulation or experiment. To aid in transparency, reproducibility, and future enhancements we have included an extensively commented Rmarkdown file and a deidentified data set.

Acetabular dysplasia is a known cause of hip osteoarthritis. In addition to abnormal anatomy, changes in kinematics, joint reaction forces (JRFs), and muscle forces could cause tissue damage to the cartilage and labrum, and may contribute to pain and fatigue. The objective of this study was to compare lower extremity joint angles, moments, hip JRFs and muscle forces during gait between patients with symptomatic acetabular dysplasia and healthy controls. Marker trajectories and ground reaction forces were measured in 10 dysplasia patients and 10 typically developing control subjects. A musculoskeletal model was scaled in OpenSim to each subject and subject-specific hip joint centers were determined using reconstructions from CT images. Joint kinematics and moments were calculated using inverse kinematics and inverse dynamics, respectively. Muscle forces and hip JRFs were estimated with static optimization. Inter-group differences were tested for statistical significance (p≤0.05) and large effect sizes (d≥0.8). Results demonstrated that dysplasia patients had higher medially directed JRFs. Joint angles and moments were mostly similar between the groups, but large inter-group effect sizes suggested some restriction in range of motion by patients at the hip and ankle. Higher medially-directed JRFs and inter-group differences in hip muscle forces likely stem from lateralization of the hip joint center in dysplastic patients. Joint force differences, combined with reductions in range of motion at the hip and ankle may also indicate compensatory strategies by patients with dysplasia to maintain joint stability.

Cardan angle sequences are widely used to describe three-dimensional joint rotations in the foot and ankle, but differences in rotation order can complicate interpretation, especially in joints with multiplanar motion. This study systematically evaluated the influence of Cardan sequence selection on the kinematics of the tibiotalar, talofibular, tibiofibular, subtalar, and talonavicular joints using both in vivo biplane fluoroscopy gait analysis and in vitro passive joint kinematic data from robotic cadaveric simulation. Six Cardan sequences were evaluated to quantify their effects on joint angle profiles and range of motion. Tibiotalar, talofibular, and tibiofibular joint kinematics were largely consistent across Cardan sequences, supporting continued use of the ISB-recommended XYZ sequence (dorsiflexion/plantarflexion followed by inversion/eversion followed by internal/external rotation). Subtalar and talonavicular joint kinematics exhibited substantial sequence-dependent variations in reported joint angles during gait, prescribed tibial external/internal rotation, and prescribed tibial varus/valgus alignment motions. Sequences prioritizing the Y-axis (inversion/eversion) or Z-axis (internal/external rotation) produced the most significant differences relative to the XYZ sequence. Based on joint- and motion-specific sensitivity, we recommend the XYZ sequence for the tibiotalar, talofibular, and tibiofibular joints; YZX, ZXY, or ZYX sequences for prioritizing transverse subtalar joint motion and XYZ or XZY sequences for coronal subtalar joint motion; and XYZ, XZY, or YXZ sequences for sagittal and transverse talonavicular joint motion, with YZX sequence for coronal talonavicular joint motion. These findings highlight the importance of joint-specific rotation sequence selection to improve consistency, reduce crosstalk, and enhance the clinical relevance of foot and ankle kinematic analyses.

Walking is an important skill with positive impacts on health, function, and well-being. Many disorders impair walking and its positive impacts through a variety of complex and interrelated mechanisms. Any attempt to understand walking impairments, or the effects of interventions intended to treat these impairments, must respect this complexity. Therefore, our main objectives in conducting this study were to (1) propose a comprehensive model for quantifying the causes and consequences of walking impairments and (2) demonstrate the potential utility of the model for supporting clinical care and addressing basic scientific questions related to walking. To achieve these goals, we introduced a model, described by a directed acyclic graph, consisting of 10 nodes and 23 primary causal paths. We gave detailed descriptions of each node and path based on domain knowledge. We then demonstrated the model’s utility using a large sample of gait data (N = 9504) acquired as part of routine care at a regional referral center. We analyzed five relevant examples that involved many of the model’s nodes and paths. We computed causal effect magnitudes as Shapley values and displayed the overall importance of variables (mean absolute Shapley value), the variation of Shapley values with respect to underlying variables, and Shapley values for individual observations (case studies). We showed that the model was plausible, captured some well-known cause-effect relationships, provided new insights into others, and generated novel hypotheses requiring further testing through simulation or experiment. To aid in transparency, reproducibility, and future enhancements we have included an extensively commented Rmarkdown file and a deidentified data set.

The crystallinity of polymers strongly affects their properties. For block copolymers, whereby two crystallisable blocks are covalently tethered to one another, the molecular weight of the individual blocks and their relative weight fraction are important structural parameters that control their crystallisation. In the case of block copolymer micelles, these parameters can influence the crystallinity of the core, which has implications for drug encapsulation and release. Therefore, in this study, we aimed to determine how the microstructure of poly(ethylene glycol-b-caprolactone) (PEG-b-PCL) copolymers contributes to the crystallinity of their hydrophobic PCL micelle cores. Using a library of PEG-b-PCL copolymers with PEG number-average molecular weight (Mn) values of 2, 5, and 10 kDa and weight fractions of PCL (fPCL) ranging from 0.11 to 0.67, the thermal behaviour and morphology were studied in blends, bulk, and micelles using differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WXRD), and Synchrotron wide-angle X-ray scattering (WAXS). Compared to PEG and PCL homopolymers, the block copolymers displayed reduced crystallinity in the bulk phase and the individual blocks had a large influence on the crystallisation of one another. The fPCL was determined to be the dominant contributor to the extent and order of crystallisation of the two blocks. When fPCL < 0.35, the initial crystallisation of PEG led to an amorphous PCL phase. At fPCL values between 0.35 and 0.65, PEG crystallisation was followed by PCL crystallisation, whereas this behaviour was reversed when fPCL > 0.65. For lyophilised PEG-b-PCL micelles, the crystallinity of the core increased with increasing fPCL, although the core was predominately amorphous for micelles with fPCL < 0.35. These findings contribute to understanding the relationships between copolymer microstructure and micelle core crystallinity that are important for the design and performance of micellar drug delivery systems, and the broader application of polymer micelles.