Gut bacterial nutrient preferences quantified in vivo.

Great progress has been made in understanding gut microbiomes' products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here, we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate, and urea (but not glucose or amino acids) feed the gut microbiome. To determine the nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.

The landscape of the methodology in drug repurposing using human genomic data: a systematic review.

The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.

Epistemic misalignments in microbiome research.

We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call "epistemic misalignment." An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole.

Scientific guidelines for evaluating the validity of forensic feature-comparison methods.

When it comes to questions of fact in a legal context-particularly questions about measurement, association, and causality-courts should employ ordinary standards of applied science. Applied sciences generally develop along a path that proceeds from a basic scientific discovery about some natural process to the formation of a theory of how the process works and what causes it to fail, to the development of an invention intended to assess, repair, or improve the process, to the specification of predictions of the instrument's actions and, finally, empirical validation to determine that the instrument achieves the intended effect. These elements are salient and deeply embedded in the cultures of the applied sciences of medicine and engineering, both of which primarily grew from basic sciences. However, the inventions that underlie most forensic science disciplines have few roots in basic science, and they do not have sound theories to justify their predicted actions or results of empirical tests to prove that they work as advertised. Inspired by the "Bradford Hill Guidelines"-the dominant framework for causal inference in epidemiology-we set forth four guidelines that can be used to establish the validity of forensic comparison methods generally. This framework is not intended as a checklist establishing a threshold of minimum validity, as no magic formula determines when particular disciplines or hypotheses have passed a necessary threshold. We illustrate how these guidelines can be applied by considering the discipline of firearm and tool mark examination.

Operando probing and adjusting of the complicated electrode process of multivalent metals at extreme temperature.

Nearly half of the elements in the periodic table are extracted, refined, or plated using electrodeposition in high-temperature melts. However, operando observations and tuning of the electrodeposition process during realistic electrolysis operations are extremely difficult due to severe reaction conditions and complicated electrolytic cell, which makes the improvement of the process very blind and inefficient. Here, we developed a multipurpose operando high-temperature electrochemical instrument that combines operando Raman microspectroscopy analysis, optical microscopy imaging, and a tunable magnetic field. Subsequently, the electrodeposition of Ti-which is a typical polyvalent metal and generally shows a very complex electrode process-was used to verify the stability of the instrument. The complex multistep cathodic process of Ti in the molten salt at 823 K was systematically analyzed by a multidimensional operando analysis strategy involving multiple experimental studies, theoretical calculations, etc. The regulatory effect and its corresponding scale-span mechanism of the magnetic field on the electrodeposition process of Ti were also elucidated, which would be inaccessible with existing experimental techniques and is significant for the real-time and rational optimization of the process. Overall, this work established a powerful and universal methodology for in-depth analysis of high-temperature electrochemistry.

Unexpected conformational variations of the human centromeric chromatin complex.

We combined classical salt fractionation with chromatin immunoprecipitation to recover human centromeric chromatin under native conditions. We found that >85% of the total centromeric chromatin is insoluble under conditions typically used for native chromatin extraction. To map both soluble and insoluble chromatin in situ, we combined CUT&RUN (cleavage under targets and release using nuclease), a targeted nuclease method, with salt fractionation. Using this approach, we observed unexpected structural and conformational variations of centromere protein A (CENP-A)-containing complexes on different α-satellite dimeric units within highly homogenous arrays. Our results suggest that slight α-satellite sequence differences control the structure and occupancy of the associated centromeric chromatin complex.

Masks and respirators for prevention of respiratory infections: a state of the science review.

SUMMARYThis narrative review and meta-analysis summarizes a broad evidence base on the benefits-and also the practicalities, disbenefits, harms and personal, sociocultural and environmental impacts-of masks and masking. Our synthesis of evidence from over 100 published reviews and selected primary studies, including re-analyzing contested meta-analyses of key clinical trials, produced seven key findings. First, there is strong and consistent evidence for airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens. Second, masks are, if correctly and consistently worn, effective in reducing transmission of respiratory diseases and show a dose-response effect. Third, respirators are significantly more effective than medical or cloth masks. Fourth, mask mandates are, overall, effective in reducing community transmission of respiratory pathogens. Fifth, masks are important sociocultural symbols; non-adherence to masking is sometimes linked to political and ideological beliefs and to widely circulated mis- or disinformation. Sixth, while there is much evidence that masks are not generally harmful to the general population, masking may be relatively contraindicated in individuals with certain medical conditions, who may require exemption. Furthermore, certain groups (notably D/deaf people) are disadvantaged when others are masked. Finally, there are risks to the environment from single-use masks and respirators. We propose an agenda for future research, including improved characterization of the situations in which masking should be recommended or mandated; attention to comfort and acceptability; generalized and disability-focused communication support in settings where masks are worn; and development and testing of novel materials and designs for improved filtration, breathability, and environmental impact.

Dynamic tandem proximity-based proteomics-Protein trafficking at the proteome-scale.

TransitID is a new methodology based on proximity labeling allowing for the study of protein trafficking a the proteome scale.

Complexity of STG signals and linguistic rhythm: a methodological study for EEG data.

The superior temporal and the Heschl's gyri of the human brain play a fundamental role in speech processing. Neurons synchronize their activity to the amplitude envelope of the speech signal to extract acoustic and linguistic features, a process known as neural tracking/entrainment. Electroencephalography has been extensively used in language-related research due to its high temporal resolution and reduced cost, but it does not allow for a precise source localization. Motivated by the lack of a unified methodology for the interpretation of source reconstructed signals, we propose a method based on modularity and signal complexity. The procedure was tested on data from an experiment in which we investigated the impact of native language on tracking to linguistic rhythms in two groups: English natives and Spanish natives. In the experiment, we found no effect of native language but an effect of language rhythm. Here, we compare source projected signals in the auditory areas of both hemispheres for the different conditions using nonparametric permutation tests, modularity, and a dynamical complexity measure. We found increasing values of complexity for decreased regularity in the stimuli, giving us the possibility to conclude that languages with less complex rhythms are easier to track by the auditory cortex.

Why postmortems fail.

Most high-profile disasters are followed by demands for an investigation into what went wrong. Even before they start, calls for finding the missed warning signs and an explanation for why people did not "connect the dots" will be common. Unfortunately, however, the same combination of political pressures and the failure to adopt good social science methods that contributed to the initial failure usually lead to postmortems that are badly flawed. The high stakes mean that powerful actors will have strong incentives to see that certain conclusions are-and are not-drawn. Most postmortems also are marred by strong psychological biases, especially the assumption that incorrect inferences must have been the product of wrong ways of thinking, premature cognitive closure, the naive use of hindsight, and the neglect of the comparative method. Given this experience, I predict that the forthcoming inquiries into the January 6, 2021, storming of the US Capitol and the abrupt end to the Afghan government will stumble in many ways.

Accelerating the discovery of novel magnetic materials using machine learning-guided adaptive feedback.

Magnetic materials are essential for energy generation and information devices, and they play an important role in advanced technologies and green energy economies. Currently, the most widely used magnets contain rare earth (RE) elements. An outstanding challenge of notable scientific interest is the discovery and synthesis of novel magnetic materials without RE elements that meet the performance and cost goals for advanced electromagnetic devices. Here, we report our discovery and synthesis of an RE-free magnetic compound, Fe3CoB2, through an efficient feedback framework by integrating machine learning (ML), an adaptive genetic algorithm, first-principles calculations, and experimental synthesis. Magnetic measurements show that Fe3CoB2 exhibits a high magnetic anisotropy (K1 = 1.2 MJ/m3) and saturation magnetic polarization (Js = 1.39 T), which is suitable for RE-free permanent-magnet applications. Our ML-guided approach presents a promising paradigm for efficient materials design and discovery and can also be applied to the search for other functional materials.

Use of chitin:DNA ratio to assess growth form in fungal cells.

BACKGROUND: Dimorphism, the ability to switch between a 'yeast-like' and a hyphal growth form, is an important feature of certain fungi, including important plant and human pathogens. The switch to hyphal growth is often associated with virulence, pathogenicity, biofilm formation and stress resistance. Thus, the ability to accurately and efficiently measure fungal growth form is key to research into these fungi, especially for discovery of potential drug targets. To date, fungal growth form has been assessed microscopically, a process that is both labour intensive and costly. RESULTS: Here, we unite quantification of the chitin in fungal cell walls and the DNA in nuclei to produce a methodology that allows fungal cell shape to be estimated by calculation of the ratio between cell wall quantity and number of nuclei present in a sample of fungus or infected host tissue. Using the wheat pathogen Zymoseptoria tritici as a test case, with confirmation in the distantly related Fusarium oxysporum, we demonstrate a close, linear relationship between the chitin:DNA ratio and the average polarity index (length/width) of fungal cells. We show the utility of the method for estimating growth form in infected wheat leaves, differentiating between the timing of germination in two different Z. tritici isolates using this ratio. We also show that the method is robust to the occurrence of thick-walled chlamydospores, which show a chitin:DNA ratio that is distinct from either 'yeast-like' blastospores or hyphae. CONCLUSIONS: The chitin:DNA ratio provides a simple methodology for determining fungal growth form in bulk tissue samples, reducing the need for labour-intensive microscopic studies requiring specific staining or GFP-tags to visualise the fungus within host tissues. It is applicable to a range of dimorphic fungi under various experimental conditions.

The dwarf neon rainbowfish Melanotaenia praecox, a small spiny-rayed fish with potential as a new Acanthomorpha model fish: II. Establishment of a microinjection procedure for genetic engineering.

BACKGROUND: Rainbowfish is a clade of colorful freshwater fish. Melanotaenia praecox is a small rainbowfish species with biological characteristics that make it potentially useful as an experimental model species. We anticipate that M. praecox could become a new model used in various fields, such as ecology, evolution, and developmental biology. However, few previous studies have described experimental set-ups needed to understand the molecular and genetic mechanisms within this species. RESULTS: We describe detailed procedures for genetic engineering in the rainbowfish M. praecox. By using these procedures, we successfully demonstrated CRISPR/Cas-mediated knockout and Tol2 transposon-mediated transgenesis in this species. Regarding the CRISPR/Cas system, we disrupted the tyrosinase gene and then showed that injected embryos lacked pigmentation over much of their body. We also demonstrated that a Tol2 construct, including a GFP gene driven by a ubiquitous promoter, was efficiently integrated into the genome of M. praecox embryos. CONCLUSIONS: The establishment of procedures for genetic engineering in M. praecox enables investigation of the genetic mechanisms behind a broad range of biological phenomena in this species. Thus, we suggest that M. praecox can be used as a new model species in various experimental biology fields.

A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus.

Mycobacterium abscessus is increasingly recognized for causing infections that are notoriously difficult to treat, owing to its large arsenal of intrinsic antibiotic resistance mechanisms. Tools for the genetic manipulation of the pathogen are critical for enabling a better understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods are largely recombination-based, which are relatively inefficient. Meanwhile, CRISPR/Cas9 has revolutionized the field of genome editing including its recent adaptation for use in mycobacteria. In this study, we report a streamlined and efficient method for rapid genetic disruptions in M. abscessus. Harnessing the CRISPR1 loci from Streptococcus thermophilus, we have developed a dual-plasmid workflow that introduces Cas9 and sgRNA cassettes in separate steps but requires no other additional factors to engineer mutations in single genes or multiple genes simultaneously or sequentially using multiple targeting sgRNAs. Importantly, the efficiency of mutant generation is several orders of magnitude higher than reported for homologous recombination-based methods. This work, thus, reports the first application of CRISPR/Cas9 for gene editing in M. abscessus and is an important tool in the arsenal for the genetic manipulation of this human pathogen. IMPORTANCE: Mycobacterium abscessus is an opportunistic pathogen of increasing clinical importance due to its poor clinical outcomes and limited treatment options. Drug discovery and development in this highly antibiotic-resistant species will require further understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods for facile genetic engineering are relatively inefficient. This study reports on the first application of CRISPR/Cas9 for gene editing in M. abscessus using a dual-plasmid workflow. We establish that our method is easily programmable, efficient, and versatile for genetic disruptions in M. abscessus. This is a critical advancement to facilitating targeted gene function studies in this emerging pathogen.

ISOLATION OF A PERSISTENTLY QUIESCENT MUSCLE SATELLITE CELL POPULATION.

While studies have identified characteristics of quiescent satellite cells, their isolation has been hampered by the fact that the isolation procedures result in the activation of these cells into their rapidly proliferating progeny (myoblasts). Thus, the use of myoblasts for therapeutic (regenerative medicine) or industrial applications (cellular agriculture) has been impeded by the limited proliferative and differentiative capacity of these myogenic progenitors. Here we identify a subpopulation of satellite cells isolated from mouse skeletal muscle using flow cytometry that are highly Pax7-positive, exhibit a very slow proliferation rate (7.7 ± 1.2 days/doubling), and are capable of being maintained in culture for at least three months without a change in phenotype. These cells can be activated from quiescence using a p38 inhibitor or by exposure to freeze-thaw cycles. Once activated, these cells proliferate rapidly (22.7 ± 0.2 hours/doubling), have reduced Pax7 expression (3-fold decrease in Pax7 fluorescence vs. quiescence) and differentiate into myotubes with a high efficiency. Furthermore, these cells withstand freeze-thawing readily without a significant loss of viability (83.1 ± 2.1% live). The results presented here provide researchers with a method to isolate quiescent satellite cells, allowing for more detailed examinations of the factors affecting satellite cell quiescence/activation and providing a cell source that has a unique potential in the regenerative medicine and cellular agriculture fields.

Identifying patterns to uncover the importance of biological pathways on known drug repurposing scenarios.

BACKGROUND: Drug repurposing plays a significant role in providing effective treatments for certain diseases faster and more cost-effectively. Successful repurposing cases are mostly supported by a classical paradigm that stems from de novo drug development. This paradigm is based on the "one-drug-one-target-one-disease" idea. It consists of designing drugs specifically for a single disease and its drug's gene target. In this article, we investigated the use of biological pathways as potential elements to achieve effective drug repurposing. METHODS: Considering a total of 4214 successful cases of drug repurposing, we identified cases in which biological pathways serve as the underlying basis for successful repurposing, referred to as DREBIOP. Once the repurposing cases based on pathways were identified, we studied their inherent patterns by considering the different biological elements associated with this dataset, as well as the pathways involved in these cases. Furthermore, we obtained gene-disease association values to demonstrate the diminished significance of the drug's gene target in these repurposing cases. To achieve this, we compared the values obtained for the DREBIOP set with the overall association values found in DISNET, as well as with the drug's target gene (DREGE) based repurposing cases using the Mann-Whitney U Test. RESULTS: A collection of drug repurposing cases, known as DREBIOP, was identified as a result. DREBIOP cases exhibit distinct characteristics compared with DREGE cases. Notably, DREBIOP cases are associated with a higher number of biological pathways, with Vitamin D Metabolism and ACE inhibitors being the most prominent pathways. Additionally, it was observed that the association values of GDAs in DREBIOP cases were significantly lower than those in DREGE cases (p-value < 0.05). CONCLUSIONS: Biological pathways assume a pivotal role in drug repurposing cases. This investigation successfully revealed patterns that distinguish drug repurposing instances associated with biological pathways. These identified patterns can be applied to any known repurposing case, enabling the detection of pathway-based repurposing scenarios or the classical paradigm.

Modeling default mode network patterns via a universal spatio-temporal brain attention skip network.

Designing a comprehensive four-dimensional resting-state functional magnetic resonance imaging (4D Rs-fMRI) based default mode network (DMN) modeling methodology to reveal the spatio-temporal patterns of individual DMN, is crucial for understanding the cognitive mechanisms of the brain and the pathogenesis of psychiatric disorders. However, there are still two limitations of existing approaches for DMN modeling. The approaches either (1) simply split the spatio-temporal components and ignore the overall character of the spatio-temporal patterns or (2) are biased in the process of feature extraction for DMN modeling, and their spatio-temporal accuracy is thus not warranted. To this end, we propose a novel Spatio-Temporal Brain Attention Skip Network (STBAS-Net) to model the personalized spatio-temporal patterns of the DMN. STBAS-Net consists of spatial and temporal components, where the multi-head attention skip connection block in the spatial component achieves detailed feature extraction and enhancement in the shallow stage. Under the guidance of spatial information, we technically fuse multiple spatio-temporal information in the temporal component, which dexterously exploits the overall spatio-temporal features and achieves mutual constraints of spatio-temporal patterns to characterize the spatio-temporal patterns of the DMN. We verify the proposed STBAS-Net on a publicly released 4D Rs-fMRI dataset and an EMCI dataset. The experimental results show that compared with existing advanced methods, the proposed network can more accurately model the personalized spatio-temporal patterns of the human brain DMN and successfully identify abnormal spatio-temporal patterns in EMCI patients. This study provides a potential tool for revealing the spatio-temporal patterns of the human brain DMN and is expected to provide an effective methodological framework for future exploration of abnormal brain spatio-temporal patterns and modeling of other functional brain networks.

Risk-management decision-making data from a community-based sample of racially diverse women at high risk of breast cancer: rationale, methods, and sample characteristics of the Daughter Sister Mother Project survey.

BACKGROUND: To understand the dynamics that limit use of risk-management options by women at high risk of breast cancer, there is a critical need for research that focuses on patient perspectives. Prior research has left important gaps: exclusion of high-risk women not in risk-related clinical care, exclusion of non-white populations, and lack of attention to the decision-making processes that underlie risk-management choices. Our objective was to create a more inclusive dataset to facilitate research to address disparities related to decision making for breast cancer risk management. METHODS: The Daughter Sister Mother Project survey collects comprehensive information about the experiences of women at high risk of breast cancer. We collected novel measures of feelings about and reactions to cancer screenings; knowledge, barriers, and facilitators of risk-management options; beliefs related to cancer risk and risk management; and involvement with loved ones who had cancer. Eligible individuals were non-Hispanic white and non-Hispanic Black adult women who self-identified as having high risk of breast cancer and had no personal history of cancer. Between October 2018 and August 2019, 1053 respondents completed the online survey. Of these, 717 were confirmed through risk prediction modeling to have a lifetime breast cancer risk of ≥ 20%. Sociodemographic characteristics of this sample were compared to those of nationally representative samples of the US population: the 2019 Health Information National Trends Survey and the Pew Research Center report: Jewish Americans in 2020. RESULTS: The sample of 717 women at objectively high risk of breast cancer was largely (95%) recruited from non-clinical sources. Of these respondents, only 31% had seen a genetic counselor, 34% had had genetic testing specific to breast cancer risk, and 35% had seen at least one breast or cancer care specialist. The sample includes 35% Black respondents and 8% with Ashkenazi Jewish ancestry. Although encompassing a substantial range of ages, incomes, and education levels, respondents are overall somewhat younger, higher-income, and more educated than the US population as a whole. CONCLUSIONS: The DSM dataset offers comprehensive data from a community-based, diverse sample of women at high risk of breast cancer. The dataset includes substantial proportions of Black and Ashkenazi Jewish women and women who are not already in clinical care related to their breast cancer risk. This sample will facilitate future studies of risk-management behaviors among women who are and are not receiving high-risk care, and of variations in risk-management experiences across race and ethnicity.

Construction of a Synergy Combination Model for Turmeric (Curcuma longa L.) and Black Pepper (Piper nigrum L.) Extracts: Enhanced Anticancer Activity against A549 and NCI-H292 Human Lung Cancer Cells.

Extensive research on medicinal herbs for bioactive compounds proposes that they could replace synthetic drugs, reducing side effects and economic burdens. Especially, interest in the synergistic benefits of natural products is increasing, implying that their combined use may enhance therapeutic effectiveness. This study aimed to explore the synergetic effects of turmeric (Curcuma longa L.) and black pepper (Piper nigrum L.) extract on lung normal (MRC-5) and cancer (A549 and NCI-H292) cell lines. The turmeric extract (TM) only affected the lung cancer cell lines, but it had no impact on the MRC-5 cell line. On the other hand, the black pepper extract (BP) did not cause any damage to either the lung normal or cancer cell lines, even at concentrations of up to 400 µg/mL. Response surface methodology was used to predict the ideal synergistic concentrations (EC50) of TM and BP, which were found to be 48.5 and 241.7 µg/mL, respectively. Notably, the selected condition resulted in higher cytotoxicity compared to the exposure to TM alone, indicating a potent synergetic effect. The rate of curcumin degradation under this combined treatment was significantly decreased to 49.72 ± 5.00 nmol/h/µg for A549 cells and 47.53 ± 4.78 nmol/h/µg for NCI-H292 cells, respectively, as compared to curcumin alone. Taken together, this study confirmed the potent synergistic effect of TM and BP on lung cancer cell lines. Further research is required to identify their specific synergetic mechanisms. Our findings provide crucial foundational data on the synergistic effects of TM and BP.

A novel approach to measure mitochondrial respiration in frozen biological samples.

Respirometry is the gold standard measurement of mitochondrial oxidative function, as it reflects the activity of the electron transport chain complexes working together. However, the requirement for freshly isolated mitochondria hinders the feasibility of respirometry in multi-site clinical studies and retrospective studies. Here, we describe a novel respirometry approach suited for frozen samples by restoring electron transfer components lost during freeze/thaw and correcting for variable permeabilization of mitochondrial membranes. This approach preserves 90-95% of the maximal respiratory capacity in frozen samples and can be applied to isolated mitochondria, permeabilized cells, and tissue homogenates with high sensitivity. We find that primary changes in mitochondrial function, detected in fresh tissue, are preserved in frozen samples years after collection. This approach will enable analysis of the integrated function of mitochondrial Complexes I to IV in one measurement, collected at remote sites or retrospectively in samples residing in tissue biobanks.