Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the RecA-(In)dependent Response to Mitomycin C in Mycobacterium tuberculosis Using Transcriptional Profiling and Proteomics Analyses

Mycobacteria exploit at least two independent global systems in response to DNA damage: the LexA/RecA-dependent SOS response and the PafBC-regulated pathway. Intracellular pathogens, such as Mycobacterium tuberculosis, are exposed to oxidative and nitrosative stress during the course of infection while residing inside host macrophages. The current understanding of RecA-independent responses to DNA damage is based on the saprophytic model of Mycobacterium smegmatis, a free-living and nonpathogenic mycobacterium. The aim of the present study was to identify elements of RecA-independent responses to DNA damage in pathogenic intracellular mycobacteria. With the help of global transcriptional profiling, we were able to dissect RecA-dependent and RecA-independent pathways. We profiled the DNA damage responses of an M. tuberculosis strain lacking the recA gene, a strain with an undetectable level of the PafBC regulatory system, and a strain with both systems tuned down simultaneously. RNA-Seq profiling was correlated with the evaluation of cell survival in response to DNA damage to estimate the relevance of each system to the overall sensitivity to genotoxic agents. We also carried out whole-cell proteomics analysis of the M. tuberculosis strains in response to mitomycin C. This approach highlighted that LexA, a well-defined key element of the SOS system, is proteolytically inactivated during RecA-dependent DNA repair, which we found to be transcriptionally repressed in response to DNA-damaging agents in the absence of RecA. Proteomics profiling revealed that AlkB was significantly overproduced in the ΔrecA pafBCCRISPRi/dCas9 strain and that Holliday junction resolvase RuvX was a DNA damage response factor that was significantly upregulated regardless of the presence of functional RecA and PafBC systems, thus falling into a third category of DNA damage factors: RecA- and PafBC-independent. While invisible to the mass spectrometer, the genes encoding alkA, dnaB, and dnaE2 were significantly overexpressed in the ΔrecA pafBCCRISPRi/dCas9 strain at the transcript level.
Plasmin, Immunity, and Surgical Site Infection

SSI are a universal economic burden and increase individual patient morbidity and mortality. While antibiotic prophylaxis is the primary preventative intervention, these agents are not themselves benign and may be less effective in the context of emerging antibiotic resistant organisms. Exploration of novel therapies as an adjunct to antimicrobials is warranted. Plasmin and the plasminogen activating system has a complex role in immune function. The immunothrombotic role of plasmin is densely interwoven with the coagulation system and has a multitude of effects on the immune system constituents, which may not always be beneficial. Tranexamic acid is an antifibrinolytic agent which inhibits the conversion of plasminogen to plasmin. Clinical trials have demonstrated a reduction in surgical site infection in TXA exposed patients, however the mechanism and magnitude of this benefit is incompletely understood. This effect may be through the reduction of local wound haematoma, decreased allogenic blood transfusion or a direct immunomodulatory effect. Large scale randomised clinical trial are currently being undertaken to better explain this association. Importantly, TXA is a safe and widely available pharmacological agent which may have a role in the reduction of SSI.
Computational Mechanisms Mediating Inhibitory Control of Coordinated Eye-Hand Movements

Significant progress has been made in understanding the computational and neural mechanisms that mediate eye and hand movements made in isolation. However, less is known about the mechanisms that control these movements when they are coordinated. Here, we outline our computational approaches using accumulation-to-threshold and race-to-threshold models to elucidate the mechanisms that initiate and inhibit these movements. We suggest that, depending on the behavioral context, the initiation and inhibition of coordinated eye-hand movements can operate in two modes—coupled and decoupled. The coupled mode operates when the task context requires a tight coupling between the effectors; a common command initiates both effectors, and a unitary inhibitory process is responsible for stopping them. Conversely, the decoupled mode operates when the task context demands weaker coupling between the effectors; separate commands initiate the eye and hand, and separate inhibitory processes are responsible for stopping them. We hypothesize that the higher-order control processes assess the behavioral context and choose the most appropriate mode. This computational mechanism can explain the heterogeneous results observed across many studies that have investigated the control of coordinated eye-hand movements and may also serve as a general framework to understand the control of complex multi-effector movements.
The Role of Inflammation in Breast and Prostate Cancer Metastasis to Bone

Tumor metastasis to bone is a common event in multiple forms of malignancy. Inflammation holds essential functions in homeostasis as a defense mechanism against infections and is a strategy to repair injured tissue and to adapt to stress conditions. However, exaggerated and/or persistent (chronic) inflammation may eventually become maladaptive and evoke diseases such as autoimmunity, diabetes, inflammatory tissue damage, fibrosis, and cancer. In fact, inflammation is now considered a hallmark of malignancy with prognostic relevance. Emerging studies have revealed a central involvement of inflammation in several steps of the metastatic cascade of bone-homing tumor cells through supporting their survival, migration, invasion, and growth. The mechanisms by which inflammation favors these steps involve activation of epithelial-to-mesenchymal transition (EMT), chemokine-mediated homing of tumor cells, local activation of osteoclastogenesis, and a positive feedback amplification of the protumorigenic inflammation loop between tumor and resident cells. In this review, we summarize established and evolving concepts of inflammation-driven tumorigenesis, with a special focus on bone metastasis.
Assessing the functional relevance of splice isoforms

Abstract Alternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.
Measuring Quality of Life Using Patient-Reported Outcomes in Real-World Metastatic Breast Cancer Patients: The Need for a Standardized Approach

Simple Summary Metastatic breast cancer (MBC) remains incurable despite treatment improvements. The health-related quality of life is a multidimensional entity which covers physical, psychological and social dimensions. It is an important outcome particularly in patients with metastatic disease, as the primary goal of therapy is no longer curation, but to provide the best possible quality of life weighted against treatment risks and adverse symptoms. Patient-reported outcomes reflecting the quality of life are usually measured with validated questionnaires to evaluate treatment strategies based on symptom burden and to improve care delivery. This review shares insights into the role of patient-reported outcome measurements in MBC patients and describes the heterogeneity of current questionnaires. We conclude that an up-to-date and standardized outcome set is needed, containing relevant domains referring to individual needs to improve the quality of life assessment among MBC patients. This is a prerequisite to learn about how they could impact the clinical care pathway. Abstract Metastatic breast cancer (MBC) patients are almost always treated to minimize the symptom burden, and to prolong life without a curative intent. Although the prognosis of MBC patients has improved in recent years, the median survival after diagnosis is still only 3 years. Therefore, the health-related quality of life (HRQoL) should play a leading role in making treatment decisions. Heterogeneity in questionnaires used to evaluate the HRQoL in MBC patients complicates the interpretability and comparability of patient-reported outcomes (PROs) globally. In this review, we aimed to provide an overview of PRO instruments used in real-world MBC patients and to discuss important issues in measuring HRQoL. Routinely collecting symptom information using PROs could enhance treatment evaluation and shared decision-making. Standardizing these measures might help to improve the implementation of PROs, and facilitates collecting and sharing data to establish valid comparisons in research. This is a prerequisite to learn about how they could impact the clinical care pathway. In addition, the prognostic value of intensified PRO collection throughout therapy on survival and disease progression is promising. Future perspectives in the field of PROs and MBC are described.
Perilla Leaf Extract Attenuates Asthma Airway Inflammation by Blocking the Syk Pathway

Perilla frutescens (L.) Britton is a classic herbal plant used widely against asthma in China. But its mechanism of beneficial effect remains undermined. In the study, the antiallergic asthma effects of Perilla leaf extract (PLE) were investigated, and the underlying mechanism was also explored. Results showed that PLE treatment significantly attenuated airway inflammation in OVA-induced asthma mice, by ameliorating lung pathological changes, inhibiting recruitment of inflammatory cells in lung tissues and bronchoalveolar lavage fluid (BALF), decreasing the production of inflammatory cytokines in the BALF, and reducing the level of immunoglobulin in serum. PLE treatment suppressed inflammatory response in antigen-induced rat basophilic leukemia 2H3 (RBL-2H3) cells as well as in OVA-induced human peripheral blood mononuclear cells (PBMCs). Furthermore, PLE markedly inhibited the expression and phosphorylation of Syk, NF-κB, PKC, and cPLA2 both in vivo and in vitro. By cotreating with inhibitors (BAY61-3606, Rottlerin, BAY11-7082, and arachidonyl trifluoromethyl ketone) in vitro, results revealed that PLE's antiallergic inflammatory effects were associated with the inhibition of Syk and its downstream signals NF-κB, PKC, and cPLA2. Collectively, the present results suggested that PLE could attenuate allergic inflammation, and its mechanism might be partly mediated through inhibiting the Syk pathway.
Genomics and Virulence of Klebsiella pneumoniae Kpnu95 ST1412 Harboring a Novel Incf Plasmid Encoding Blactx-M-15 and Qnrs1 Causing Community Urinary Tract Infection

The emergence of extended-spectrum β-lactamase (ESBL)-producing multidrug resistant Klebsiella pneumoniae causing community urinary tract infections (CA-UTI) in healthy women undermines effective treatment and poses a public health concern. We performed a comprehensive genomic analysis (Illumina and MinION) and virulence studies using Caenorhabditis elegans nematodes to evaluate KpnU95, a blaCTX-M-15-producing CA-UTI K. pneumoniae strain. Whole genome sequencing identified KpnU95 as sequence type 1412 and revealed the chromosomal and plasmid-encoding resistome, virulome and persistence features. KpnU95 possess a wide virulome and caused complete C. elegans killing. The strain harbored a single novel 180.3Kb IncFIB(K) plasmid (pKpnU95), which encodes ten antibiotic resistance genes, including blaCTX-M-15 and qnrS1 alongside a wide persistome encoding heavy metal and UV resistance. Plasmid curing and reconstitution were used for loss and gain studies to evaluate its role on bacterial resistance, fitness and virulence. Plasmid curing abolished the ESBL phenotype, decreased ciprofloxacin MIC and improved bacterial fitness in artificial urine accompanied with enhanced copper tolerance, without affecting bacterial virulence. Meta-analysis supported the uniqueness of pKpnU95 and revealed plasmid-ST1412 lineage adaptation. Overall, our findings provide translational data on a CA-UTI K. pneumoniae ST1412 strain and demonstrates that ESBL-encoding plasmids play key roles in multidrug resistance and in bacterial fitness and persistence.
Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans with Emphasis on CoQ10 Biosynthesis

Simple Summary We lack studies investigating mitochondrial metabolism in the prenatal and early postnatal period in humans, but parallel experiments conducted in a mammalian system are informative about the human condition. Our aim was to study the perinatal metabolic switch in rats—an extremely complex process, associated with tissue proliferation and differentiation together with a rapid oxidative stress response (using techniques including microarrays, qPCR, spectrophotometry and high-performance liquid chromatography). Out of 1546 mitochondrial genes, 1119 and 827 genes significantly changed expression in rat liver and skeletal muscle, respectively. The most remarkable expression shift occurred in the rat liver at least two days before birth. Coenzyme Q and mitochondrial metabolism-based evaluation in both the rat model and human tissues showed the same trend: the total CoQ content and mitochondrial metabolism significantly increases after birth, possibly regulated by COQ8A kinase. Our microarray data could serve as a suitable background for finding key factors regulating mitochondrial metabolism and preparation of the foetus for the transition to extra-uterine conditions, or as preliminary data for further studies of the complex mitochondrial metabolism regulation and diagnostics of mitochondrial disorders. Abstract At the end of the mammalian intra-uterine foetal development, a rapid switch from glycolytic to oxidative metabolism must proceed. Using microarray techniques, qPCR, enzyme activities and coenzyme Q content measurements, we describe perinatal mitochondrial metabolism acceleration in rat liver and skeletal muscle during the perinatal period and correlate the results with those in humans. Out of 1546 mitochondrial genes, we found significant changes in expression in 1119 and 827 genes in rat liver and skeletal muscle, respectively. The most remarkable expression shift occurred in the rat liver at least two days before birth. Coenzyme Q-based evaluation in both the rat model and human tissues showed the same trend: the total CoQ content is low prenatally, significantly increasing after birth in both the liver and skeletal muscle. We propose that an important regulator of rat coenzyme Q biosynthesis might be COQ8A, an atypical kinase involved in the biosynthesis of coenzyme Q. Our microarray data, a total of 16,557 RefSeq (Entrez) genes, have been deposited in NCBI’s Gene Expression Omnibus and are freely available to the broad scientific community. Our microarray data could serve as a suitable background for finding key factors regulating mitochondrial metabolism and the preparation of the foetus for the transition to extra-uterine conditions.
The Cortical “Upper Motoneuron” in Health and Disease

Upper motoneurons (UMNs) in motor areas of the cerebral cortex influence spinal and cranial motor mechanisms through the corticospinal tract (CST) and through projections to brainstem motor pathways. The primate corticospinal system has a diverse cortical origin and a wide spectrum of fibre diameters, including large diameter fibres which are unique to humans and other large primates. Direct cortico-motoneuronal (CM) projections from the motor cortex to arm and hand motoneurons are a late evolutionary feature only present in dexterous primates and best developed in humans. CM projections are derived from a more restricted cortical territory (‘new’ M1, area 3a) and arise not only from corticospinal neurons with large, fast axons but also from those with relatively slow-conducting axons. During movement, corticospinal neurons are organised and recruited quite differently from ‘lower’ motoneurons. Accumulating evidence strongly implicates the corticospinal system in the early stages of ALS, with particular involvement of CM projections to distal limb muscles, but also to other muscle groups influenced by the CM system. There are important species differences in the organisation and function of the corticospinal system, and appropriate animal models are needed to understand disorders involving the human corticospinal system.
Ontogenetic Variation in the Mineral, Phytochemical and Yield Attributes of Brassicaceous Microgreens

Microgreens constitute novel gastronomic ingredients that combine visual, kinesthetic and bioactive qualities. The definition of the optimal developmental stage for harvesting microgreens remains fluid. Their superior phytochemical content against mature leaves underpins the current hypothesis of significant changes in compositional profile during the brief interval of ontogeny from the appearance of the first (S1) to the second true leaf (S2). Microgreens of four brassicaceous genotypes (Komatsuna, Mibuna, Mizuna and Pak Choi) grown under controlled conditions and harvested at S1 and S2 were appraised for fresh and dry yield traits. They were further analyzed for macro- and micromineral content using inductively coupled plasma optical emission spectrometry (ICP-OES), carotenoid content using high-performance liquid chromatography with a diode-array detector (HPLC-DAD), volatile organic compounds using solid-phase microextraction followed by gas chromatography-mass spectrometry (SPME-GC/MS), anthocyanins and polyphenols using liquid chromatography-high resolution-tandem mass spectrometry (LC-MS/MS) with Orbitrap technology and for chlorophyll and ascorbate concentrations, well as antioxidant capacity by spectrophotometry. Analysis of compositional profiles revealed genotype as the principal source of variation for all constituents. The response of mineral and phytochemical composition and of antioxidant capacity to the growth stage was limited and largely genotype-dependent. It is, therefore, questionable whether delaying harvest from S1 to S2 would significantly improve the bioactive value of microgreens while the cost-benefit analysis for this decision must be genotype-specific. Finally, the lower-yielding genotypes (Mizuna and Pak Choi) registered higher relative increase in fresh yield between S1 and S2, compared to the faster-growing and higher-yielding genotypes. Although the optimal harvest stage for specific genotypes must be determined considering the increase in yield against reduction in crop turnover, harvesting at S2 seems advisable for the lower-yielding genotypes.
Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study

A carboxylated adenosine analog (C-Ado−) has been synthesized and probed via time-resolved photoelectron spectroscopy in order to induce intra-molecular charge transfer from the carboxylic acid moiety to the nucleobase. Intra-molecular charge transfer can be exploited as starting point to probe low-energy electron (LEE) damage in DNA and its derivatives. Time-dependent density functional theory (TD-DFT) calculations at the B3LYP-6311G level of theory have been performed to verify that the highest occupied molecular orbital (HOMO) was located on carboxylic acid and that the lowest occupied molecular orbital (LUMO) was on the nucleobase. Hence, the carboxylic acid could work as electron source, whilst the nucleobase could serve the purpose of electron acceptor. The dynamics following excitation at 4.66 eV (266 nm) were probed using time-resolved photoelectron spectroscopy using probes at 1.55 eV (800 nm) and 3.10 eV (400 nm). The data show rapid decay of the excited state population and, based on the similarity of the overall dynamics to deoxy-adenosine monophosphate (dAMP–), it appears that the dominant decay mechanism is internal conversion following 1ππ* excitation of the nucleobase, rather than charge-transfer from the carboxylic acid to the nucleobase.
Tropical Beef: Is There an Axiomatic Basis to Define the Concept?

Cattle production in tropical regions has been estimated to account for just over half of cattle worldwide, yet it has not been demonstrated that sufficient similarities in the cattle exist to describe tropical cattle and, even less so, to characterize the meat from these animals. The aim of this review is to investigate the quality and nutrient composition of meat from cattle raised in the Tropics to determine if there is an axiomatic basis that would allow the definition of a concept of “tropical beef”. Tropical beef is the meat obtained from cattle raised in tropical environments, the population of which remains largely uncharacterized. Production systems in the Tropics are highly diverse but converge on the use of indigenous and Bos indicus breeds or Bos indicus-influenced crossbreeds under pasture feeding regimes. While some systems allow cattle to be slaughtered at ≤2 years of age, most often animals are ≥3 years. These production systems generally produce lean, low-yielding carcasses and tough (>46 N), lean (≤3.6% intramuscular fat) meat with a macronutrient composition otherwise similar to beef from animals raised elsewhere (72–74% moisture and 20–24% protein). Fatty acid profiles depend on the breed and production systems, while mineral content is influenced by the environment. Although lean and tough, tropical beef is highly acceptable to the consumers it serves, is culturally and traditionally relevant and, in many countries, contributes to food security. Consolidating the findings from animal and meat science studies in the Tropics has allowed the demonstration of an axiomatic basis defining “tropical beef” as a concept.