In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of ...DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.
A method is described for the prediction of breeding values incorporating genomic information. The first stage involves the prediction of genomic breeding values for genotyped individuals. A novel ...component of this is the estimation of the genomic relationship matrix in the context of a multi-breed population. Because not all ancestors of genotyped animals are genotyped, a selection index procedure is used to blend genomic predictions with traditional ancestral information that is lost between the process of deregression of the national breeding values and subsequent re-estimation using the genomic relationship matrix. Finally, the genomically enhanced predictions are filtered through to nongenotyped descendants using a regression procedure.
Abstract Hypoxia is a feature of most solid tumours and is associated with a poor prognosis. The hypoxic environment can reduce the efficacy of radiotherapy and some chemotherapeutics, and has been ...investigated extensively as a therapeutic target. The clinical use of hypoxia-targeting treatment will benefit from the development of a biomarker to assess tumour hypoxia. There are several possible techniques that measure either the level of oxygen or the tumour molecular response to hypoxia. The latter includes gene expression profiling, which measures the transcriptional response of a tumour to its hypoxic microenvironment. A systematic review identified 32 published hypoxia gene expression signatures. The methods used for their derivation varied, but are broadly classified as: (i) identifying genes with significantly higher or lower expression in cancer cells cultured under hypoxic versus normoxic conditions; (ii) using either previously characterised hypoxia-regulated genes/biomarkers to define hypoxic tumours and then identifying other genes that are over- or under-expressed in the hypoxic tumours. Both generated gene signatures useful in furthering our understanding of hypoxia biology. However, signatures derived using the second method seem to be superior in terms of providing prognostic information. Here we summarise all 32 published hypoxia signatures, discuss their commonalities and differences, and highlight their strengths and limitations. This review also highlights the importance of reproducibility and gene annotation, which must be accounted for to transfer signatures robustly for clinical application as biomarkers.
Research in reintroduction biology has provided a greater understanding of the often limited success of species reintroductions and highlighted the need for scientifically rigorous approaches in ...reintroduction programs. We examined the recent genetic-based captive-breeding and reintroduction literature to showcase the underuse of the genetic data gathered. We devised a framework that takes full advantage of the genetic data through assessment of the genetic makeup of populations before (past component of the framework), during (present component), and after (future component) captive-breeding and reintroduction events to understand their conservation potential and maximize their success. We empirically applied our framework to two small fishes: Yarra pygmy perch (Nannoperca obscura) and southern pygmy perch (Nannoperca australis). Each of these species has a locally adapted and geographically isolated lineage that is endemic to the highly threatened lower Murray-Darling Basin in Australia. These two populations were rescued during Australia's recent decade-long Millennium Drought, when their persistence became entirely dependent on captive-breeding and subsequent reintroduction efforts. Using historical demographic analyses, we found differences and similarities between the species in the genetic impacts of past natural and anthropogenic events that occurred in situ, such as European settlement (past component). Subsequently, successful maintenance of genetic diversity in captivity—despite skewed brooder contribution to offspring—was achieved through carefully managed genetic-based breeding (present component). Finally, genetic monitoring revealed the survival and recruitment of released captive-bred offspring in the wild (future component). Our holistic framework often requires no additional data collection to that typically gathered in genetic-based breeding programs, is applicable to a wide range of species, advances the genetic considerations of reintroduction programs, and is expected to improve with the use of next-generation sequencing technology. Investigaciones sobre biología de la reintroducción han proporcionado un mejor entendimiento del, a menudo, éxito limitado de las reintroducciones de especies y han resaltado la necesidad de aproximaciones rigorosas científicamente en los programas de reintroducción. Examinamos la literatura reciente sobre reproducción en cautiverio basada en genética y reintroducción para exhibir la subutilización de los datos genéticos. Diseñamos un marco de referencia que obtiene la mayor ventaja de los datos genéticos mediante la evaluación de la composición genética de las poblaciones antes (componente pasado del marco de referencia), durante (componente presente), y después (componente futuro) de eventos de reproducción en cautiverio y de reintroducción para entender su potencial de conservación y maximizar su éxito. Aplicamos nuestro marco de referencia empíricamente con dos especies de peces pequeños: Nannoperca obscura y N. australis. Cada especie tiene un linaje adaptado localmente y aislado geográficamente endémico de la muy amenazada Cuenca Baja Murray-Darling, Australia. Las dos poblaciones fueron rescatadas durante la reciente Sequía del Milenio que duró diez años en Australia, cuando su persistencia se volvió totalmente dependiente de esfuerzos de reproducción en cautiverio y subsecuente reintroducción. Mediante análisis demográficos históricos, encontramos diferencias y similitudes entre las especies en los impactos genéticos de eventos naturales y antropogénicos pasados que ocurrieron in situ, como el asentamiento europeo (componente pasado). Subsecuentemente, el mantenimiento exitoso de la diversidad genética en cautiverio - no obstante la contribución de reproductores sesgada - fue posible por el manejo cuidadoso de la reproducción basada en genética (componente presente). Finalmente, el monitoreo genético reveló la supervivencia y reclutamiento de crías obtenidas en cautiverio liberadas en el medio silvestre. Nuestro marco de referencia holístico a menudo no requiere de datos adicionales a los obtenidos típicamente en programas de reproducción basados en genética, es aplicable a un rango amplio de especies, es un avance en las consideraciones genéticas de los programas de reintroducción, y mejorará con el uso de tecnología de secuenciación de última generación.
Segmental duplications at breakpoints (BP4-BP5) of chromosome 15q13.2q13.3 mediate a recurrent genomic imbalance syndrome associated with mental retardation, epilepsy, and/or electroencephalogram ...(EEG) abnormalities.
DNA samples from 1445 unrelated patients submitted consecutively for clinical array comparative genomic hybridisation (CGH) testing at Children's Hospital Boston and DNA samples from 1441 individuals with autism from 751 families in the Autism Genetic Resource Exchange (AGRE) repository.
We report the clinical features of five patients with a BP4-BP5 deletion, three with a BP4-BP5 duplication, and two with an overlapping but smaller duplication identified by whole genome high resolution oligonucleotide array CGH. These BP4-BP5 deletion cases exhibit minor dysmorphic features, significant expressive language deficits, and a spectrum of neuropsychiatric impairments that include autism spectrum disorder, attention deficit hyperactivity disorder, anxiety disorder, and mood disorder. Cognitive impairment varied from moderate mental retardation to normal IQ with learning disability. BP4-BP5 covers approximately 1.5 Mb (chr15:28.719-30.298 Mb) and includes six reference genes and 1 miRNA gene, while the smaller duplications cover approximately 500 kb (chr15:28.902-29.404 Mb) and contain three reference genes and one miRNA gene. The BP4-BP5 deletion and duplication events span CHRNA7, a candidate gene for seizures. However, none of these individuals reported here have epilepsy, although two have an abnormal EEG.
The phenotype of chromosome 15q13.2q13.3 BP4-BP5 microdeletion/duplication syndrome may include features of autism spectrum disorder, a variety of neuropsychiatric disorders, and cognitive impairment. Recognition of this broader phenotype has implications for clinical diagnostic testing and efforts to understand the underlying aetiology of this syndrome.
Display omitted
•Genomic evaluations for crossbreed dairy cattle from a New Zealand perspective are discussed.•This review provides a short history of the across-breed genetic or genomic evaluations ...used in New Zealand since 1996.•Implementation details for the current across-breed single-step marker model are outlined.
This short review discusses genomic evaluations for crossbreed dairy cattle from a New Zealand perspective. I briefly introduce the cow population and farm systems that have resulted in high crossbreeding rates and provide a short history of across-breed genetic and genomic evaluations used in New Zealand since 1996. I provide implementation details for the current across-breed single-step marker model (SSMM), including data sizes, solving methods, and how to account for multiple breed and breed crosses, along with a summary of the validation results. Finally, I outline future research areas that are being undertaken to improve our across-breed genomic evaluation.
This critical review introduces a template that links phosphorus (P) sources and mobilisation processes to the delivery of P to receiving waters where deleterious impact is of concern. It therefore ...serves as a key introductory paper in this special issue. The entire process is described in terms of a ‘P transfer continuum’ to emphasise the interdisciplinary and inter-scale nature of the problem. Most knowledge to date is derived from mechanistic studies on the sources and mobilisation of P using controlled experiments that have formed the basis for mitigation strategies aimed at minimising transfer from agricultural fields. However, our ability to extrapolate this information to larger scales is limited by a poor knowledge base while new conceptual advances in the areas of complex systems and fractal dynamics indicate the limitations of past theoretical frameworks. This is compounded by the conceptual and physical separation of scientists working at different scales within the terrestrial and aquatic sciences. Multi-scaled approaches are urgently required to integrate different disciplines and provide a platform to develop mechanistic modelling frameworks, collect new data and identify critical research questions.
Background. In older adults, there is often substantial undiagnosed chronic disease detectable on noninvasive testing, not accounted for by most comorbidity indices. We developed a simple physiologic ...index of comorbidity by scoring five noninvasive tests across the full range of values. We examined the predictive validity of this index for mortality and disability. Methods. There were 2928 (mean age 74.5 years, 60% women, 85% white, and 15% black) participants in the Cardiovascular Health Study (1992–1993) who had carotid ultrasound, pulmonary function testing, brain magnetic resonance scan, serum cystatin-C, and fasting glucose. These were combined into a single physiologic index of comorbid chronic disease on a scale of 0–10. Cox proportional hazard models were used to predict mortality, mobility limitation, and activities of daily living (ADL) difficulty after a maximum of 9 years. Results. The range of the physiologic index was quite broad, with very few individuals having total scores of either 0 or 10. Those with an index of 7–10 had a hazard ratio of 3.80 (95% confidence interval, 2.82-5.13) for mortality compared to those with scores of 0–2, after adjustment for demographics, behavioral risk factors, and clinically diagnosed conditions. Associations with mobility limitation and ADL difficulty were also significant. The index explained about 40% of the age effect on mortality risk. Conclusion. Older adults with low levels of markers of chronic disease are rather rare but have remarkably good health outcomes. The ability of such an index to distinguish usual from low risk might provide an opportunity to better understand optimal health in old age.
The Mars 2020/Mars Sample Return (MSR) Sample Depot Science Community Workshop was held on September 28 and 30, 2022, to assess the Scientifically‐Return Worthy (SRW) value of the full collection of ...samples acquired by the rover Perseverance at Jezero Crater, and of a proposed subset of samples to be left as a First Depot at a location within Jezero Crater called Three Forks. The primary outcome of the workshop was that the community is in consensus on the following statement: The proposed set of ten sample tubes that includes seven rock samples, one regolith sample, one atmospheric sample, and one witness tube constitutes a SRW collection that: (1) represents the diversity of the explored region around the landing site, (2) covers partially or fully, in a balanced way, all of the International MSR Objectives and Samples Team scientific objectives that are applicable to Jezero Crater, and (3) the analyses of samples in this First Depot on Earth would be of fundamental importance, providing a substantial improvement in our understanding of Mars. At the conclusion of the meeting, there was overall community support for forming the First Depot as described at the workshop and placing it at the Three Forks site. The community also recognized that the diversity of the Rover Cache (the sample collection that remains on the rover after placing the First Depot) will significantly improve with the samples that are planned to be obtained in the future by the Perseverance rover and that the Rover Cache is the primary target for MSR to return to Earth.
Accurate and timely pregnancy diagnosis is an important component of effective herd management in dairy cattle. Predicting pregnancy from Fourier-transform mid-infrared (FT-MIR) spectroscopy data is ...of particular interest because the data are often already available from routine milk testing. The purpose of this study was to evaluate how well pregnancy status could be predicted in a large data set of 1,161,436 FT-MIR milk spectra records from 863,982 mixed-breed pasture-based New Zealand dairy cattle managed within seasonal calving systems. Three strategies were assessed for defining the nonpregnant cows when partitioning the records according to pregnancy status in the training population. Two of these used records for cows with a subsequent calving only, whereas the third also included records for cows without a subsequent calving. For each partitioning strategy, partial least squares discriminant analysis models were developed, whereby spectra from all the cows in 80% of herds were used to train the models, and predictions on cows in the remaining herds were used for validation. A separate data set was also used as a secondary validation, whereby pregnancy diagnosis had been assigned according to the presence of pregnancy-associated glycoproteins (PAG) in the milk samples. We examined different ways of accounting for stage of lactation in the prediction models, either by including it as an effect in the prediction model, or by pre-adjusting spectra before fitting the model. For a subset of strategies, we also assessed prediction accuracies from deep learning approaches, utilizing either the raw spectra or images of spectra. Across all strategies, prediction accuracies were highest for models using the unadjusted spectra as model predictors. Strategies for cows with a subsequent calving performed well in herd-independent validation with sensitivities above 0.79, specificities above 0.91 and area under the receiver operating characteristic curve (AUC) values over 0.91. However, for these strategies, the specificity to predict nonpregnant cows in the external PAG data set was poor (0.002–0.04). The best performing models were those that included records for cows without a subsequent calving, and used unadjusted spectra and days in milk as predictors, with consistent results observed across the training, herd-independent validation and PAG data sets. For the partial least squares discriminant analysis model, sensitivity was 0.71, specificity was 0.54 and AUC values were 0.68 in the PAG data set; and for an image-based deep learning model, the sensitivity was 0.74, specificity was 0.52 and the AUC value was 0.69. Our results demonstrate that in pasture-based seasonal calving herds, confounding between pregnancy status and spectral changes associated with stage of lactation can inflate prediction accuracies. When the effect of this confounding was reduced, prediction accuracies were not sufficiently high enough to use as a sole indicator of pregnancy status.
PDF
