Search

ABSTRACT Three-dimensional chromatin organization varies across cell types and is essential for gene regulation. However, current technologies are unable to assess in vivo genome-wide chromatin organization non-invasively. Here we show that distant correlations in the fragment length of cell-free DNA (cfDNA) recapitulate three-dimensional chromatin organization. The inferred organization is highly concordant with that measured by Hi-C in white blood cells from healthy donors, and is not explained by technical bias or sequence composition. Furthermore, the inferred organization reflects different genomic organization in the various cell types contributing to cfDNA, allowing identification and quantification of tissues of origin. This approach is concordant with previous methods, but with more complete representations of cfDNA. Our results, demonstrated in cfDNA from healthy individuals and cancer patients, may enable noninvasive monitoring of in vivo genome organization and accurate quantification of cell death in different clinical conditions.

ABSTRACT Three-dimensional chromatin organization varies across cell types and is essential for gene regulation. However, current technologies are unable to assess in vivo genome-wide chromatin organization non-invasively. Here we show that distant correlations in the fragment length of cell-free DNA (cfDNA) recapitulate three-dimensional chromatin organization. The inferred organization is highly concordant with that measured by Hi-C in white blood cells from healthy donors, and is not explained by technical bias or sequence composition. Furthermore, the inferred organization reflects different genomic organization in the various cell types contributing to cfDNA, allowing identification and quantification of tissues of origin. This approach is concordant with previous methods, but with more complete representations of cfDNA. Our results, demonstrated in cfDNA from healthy individuals and cancer patients, may enable noninvasive monitoring of in vivo genome organization and accurate quantification of cell death in different clinical conditions.

The continued scaling of genetic perturbation technologies combined with high-dimensional assays such as cellular microscopy and RNA-sequencing has enabled genome-scale reverse-genetics experiments that go beyond single-endpoint measurements of growth or lethality. Datasets emerging from these experiments can be combined to construct perturbative "maps of biology", in which readouts from various manipulations (e.g., CRISPR-Cas9 knockout, CRISPRi knockdown, compound treatment) are placed in unified, relatable embedding spaces allowing for the generation of genome-scale sets of pairwise comparisons. These maps of biology capture known biological relationships and uncover new associations which can be used for downstream discovery tasks. Construction of these maps involves many technical choices in both experimental and computational protocols, motivating the design of benchmark procedures to evaluate map quality in a systematic, unbiased manner. Here, we (1) establish a standardized terminology for the steps involved in perturbative map building, (2) introduce key classes of benchmarks to assess the quality of such maps, (3) construct 18 maps from four genome-scale datasets employing different cell types, perturbation technologies, and data readout modalities, (4) generate benchmark metrics for the constructed maps and investigate the reasons for performance variations, and (5) demonstrate utility of these maps to discover new biology by suggesting roles for two largely uncharacterized genes. Author summary: Due to the rapid advancements in genetic perturbation, laboratory robotics, sequencing, and computer vision, more researchers are now generating datasets that capture cellular responses to genetic perturbations. These datasets can be powerful discovery tools for examining known biological relationships and revealing new associations in an unbiased manner when paired with a computational pipeline that can assemble the data into a digestible format. However, the challenge arises from the variety of cellular models, assay designs, terminologies, codebases, and analysis methods involved. In this work we define a unified framework for building and benchmarking perturbative maps, benchmark four different datasets assembled into 18 different maps, explore the impact of different design decisions, and demonstrate how these maps can be used to elucidate gene functions. Our goal is to facilitate comparisons across various technologies and methods by introducing a shared language for the field. The open-source codebase, capable of incorporating new methods, aims to be a resource for researchers developing laboratory or computational methodology. While we caution against definitive recommendations due to numerous variables at play, we hope to stimulate studies directly comparing methods under controlled conditions. Our framework can also help evaluate combining maps across modalities as the field progresses. [ABSTRACT FROM AUTHOR]

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Background: Crohn′s disease is being increasingly reported from Saudi Arabia and information about its pattern is still accumulating. Aim of the study: To describe and classify the disease and assess the response to therapy in patients referred to a tertiary care centre in Gassim region, Kingdom of Saudi Arabia (KSA). Patients and Methods: Fifteen Saudi patients found to have Crohn′s disease over an eight-year period were studied. The presenting symptoms, area of involvement and the response to therapy were assessed. Results: There were five males and ten females. The age of 14 patients was less than 40 years. Symptoms had existed for more than one year before diagnosis in 14 patients. Common symptoms were diarrhea, pain during defecation, blood in stool and weight loss. The ileum was involved in three patients, the colon in four and the involvement was ileocolonic in eight patients. The behavior of the disease was non-stricturing nonpenetrating in eight, stricturing in two, penetrating in one and stricturing as well as penetrating in four patients. Three patients presented as acute appendicitis, four as intestinal obstruction and five with perianal disease. Histological diagnosis was possible in 12 patients. Thrombocytosis was present in seven patients and three had episodes of deep vein thrombosis. Eight patients responded to medical therapy. Surgical intervention was necessary in seven patients and three had multiple operations. One patient died during a median follow-up period of 18 months (range: 6 months to 8 years). Conclusion: Crohn′s disease occurs more commonly in young Saudi females. Patients are symptomatic for almost a year prior to diagnosis. The presentation is variable and response to therapy is satisfactory. Surgery is necessary in a high number of patients

Background: Ulcerative colitis (UC) is being reported more frequently among the Arabs. Information on the clinical severity, endoscopic and histological grading is scanty. Aim: To assess the severity of the disease and its response to therapy in patients referred to a tertiary care referral centre in Gassim region, Kingdom of Saudi Arabia (KSA). Patients and Method: Hospital records of thirty-four patients found to have UC from 1990-2002 were analyzed. The study included clinical severity, endoscopical and histological assessment, response to therapy and frequency of complications. Results: There were 21 males and 13 females with median age 35 (range: 18-76) years. The disease was clinically mild in seven patients (21%), moderate in 11 (32%) and severe in 16 (47%). Endoscopically UC was graded as 2 in three patients (9%), 3 in 21 patients (59%) and 4 in ten patients (29%). Histologically UC was mild to moderate in 11 patients (32%) and severe in 23 (68%). Extent of UC was total in nine patients (26%), up to transverse colon in six (18%), splenic flexure in 14 (41%), rectosigmoid region in four (12%) and only up to the rectum in one (3%). Twenty-nine patients (85%) were treated with salazopyrine and five patients (15%); (two of them were hypersensitive to salazopyrine) received 5-aminosalicylic acid. Proctocolectomy was performed in two with a focus of malignancy. No patient died during the median follow-up period of 48 months (range: 4 months to 12 years). Conclusion: Ulcerative colitis presented with varying severity, more frequently in males in the population studied. Most of the patients responded to salazopyrine and surgery was necessary when malignancy was detected

We have carried out extensive all atom explicit solvent simulations of the high-temperature folding and unfolding of the trpzip2 β-hairpin peptide and examined the resulting trajectories for evidence of folding via a reptation mechanism. Over 300 microcanonical simulations of 10 ns each were initiated from a Boltzmann ensemble of conformations at 425 K. Though we observed numerous folding and unfolding events, no evidence of reptation was found. The diffusional dynamics of the peptide are orders of magnitude faster than any observed reptation-like motion. Our data suggest that the dominant mechanisms for β-hairpin folding under these conditions are hydrophobic collapse and turn formation, and that rearrangements occur via significant expansion of the polypeptide chain. [ABSTRACT FROM AUTHOR]