CD10 expression as a potential predictor of pathological complete response in ER-negative and triple-negative breast cancer patients treated with anthracycline-based neoadjuvant chemotherapy.

BACKGROUND: Neoadjuvant chemotherapy (NCT) can induce a pathological complete response (pCR) in breast cancer patients, leading to improved outcomes. However, predicting which patients will achieve pCR remains a challenge. CD10, a myoepithelial marker, has shown diagnostic and prognostic value in metastatic tumors. Its potential as a predictor of chemosensitivity to anthracycline-based NCT in breast cancer is unknown. AIM: This retrospective study aimed to investigate the potential of CD10 cancer cell expression as a predictive marker of chemosensitivity in breast cancers treated with anthracycline-based neoadjuvant chemotherapy. METHODS: We analyzed 130 patients with invasive ductal carcinoma who received anthracycline-based NCT. CD10 expression was assessed by immunohistochemistry on pre-treatment biopsies. Statistical analysis evaluated the association between CD10 expression and pCR rates. RESULTS: Univariate analysis revealed that ER-positive and CD10-negative tumors had lower pCR rates [OR 7.4830 (95% CI 2.7762-20.1699); p = 0.0001]. Multivariate analysis confirmed ER status as a strong predictor of poor response [OR 0.085 (95% CI 0.024-0.30); p < 0.001] and CD10 expression as a predictor of a favourable response [OR 0.11 (0.8-0.19); p = 0.049]. CD10 expression significantly predicted pCR in ER-negative cases [OR 0.1098 (0.0268-0.4503); p = 0.0022] and triple-negative breast cancer [OR 0.0966 (95% CI 0.0270-0.3462); p = 0.0003]. Concordance was observed between core biopsies and excised samples. CONCLUSION: Positive CD10 cancer cell expression may predict increased response to anthracycline-based neoadjuvant chemotherapy in ER-negative and triple-negative breast cancer cases. Further research is needed to validate these findings in larger cohorts and determine the clinical utility of CD10 as a predictive marker.

Precision Medicine in Castration-Resistant Prostate Cancer: Advances, Challenges, and the Landscape of PARPi Therapy-A Narrative Review.

After recent approvals, poly-adenosine diphosphate [ADP]-ribose polymerase inhibitors (PARPis) have emerged as a frontline treatment for metastatic castration-resistant prostate cancer (mCRPC). Unlike their restricted use in breast or ovarian cancers, where approval is limited to those with BRCA1/2 alterations, PARPis in mCRPC are applied across a broader spectrum of genetic aberrations. Key findings from the phase III PROPEL trial suggest that PARPis' accessibility may broaden, even without mandatory testing. An increasing body of evidence underscores the importance of distinct alterations in homologous recombination repair (HRR) genes, revealing unique sensitivities to PARPis. Nonetheless, despite the initial effectiveness of PARPis in treating BRCA-mutated tumors, resistance to therapy is frequently encountered. This review aims to discuss patient stratification based on biomarkers and genetic signatures, offering insights into the nuances of first-line PARPis' efficacy in the intricate landscape of mCRPC.

Late Health Effects of Partial Body Irradiation Injury in a Minipig Model Are Associated with Changes in Systemic and Cardiac IGF-1 Signaling.

Clinical, epidemiological, and experimental evidence demonstrate non-cancer, cardiovascular, and endocrine effects of ionizing radiation exposure including growth hormone deficiency, obesity, metabolic syndrome, diabetes, and hyperinsulinemia. Insulin-like growth factor-1 (IGF-1) signaling perturbations are implicated in development of cardiovascular disease and metabolic syndrome. The minipig is an emerging model for studying radiation effects given its high analogy to human anatomy and physiology. Here we use a minipig model to study late health effects of radiation by exposing male Göttingen minipigs to 1.9-2.0 Gy X-rays (lower limb tibias spared). Animals were monitored for 120 days following irradiation and blood counts, body weight, heart rate, clinical chemistry parameters, and circulating biomarkers were assessed longitudinally. Collagen deposition, histolopathology, IGF-1 signaling, and mRNA sequencing were evaluated in tissues. Our findings indicate a single exposure induced histopathological changes, attenuated circulating IGF-1, and disrupted cardiac IGF-1 signaling. Electrolytes, lipid profiles, liver and kidney markers, and heart rate and rhythm were also affected. In the heart, collagen deposition was significantly increased and transforming growth factor beta-1 (TGF-beta-1) was induced following irradiation; collagen deposition and fibrosis were also observed in the kidney of irradiated animals. Our findings show Göttingen minipigs are a suitable large animal model to study long-term effects of radiation exposure and radiation-induced inhibition of IGF-1 signaling may play a role in development of late organ injuries.

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

The increase in surface EMG could be a misleading measure of neural adaptation during the early gains in strength.

PURPOSE: To test the validity of using the increase in surface EMG as a measure of neural adaptation during the early gains in strength. METHODS: Simulation of EMG signals detected by surface bipolar electrode with 20-mm inter-pole distance at different radial distances from the muscle and longitudinal distances from the end-plate area. The increases in the root mean square (RMS) of the EMG signal due to possible alteration in the neural drive or elevation of the intracellular negative after-potentials, detected in fast fatigable muscle fibres during post-tetanic potentiation and assumed to accompany post-activation potentiation, were compared. RESULTS: Lengthening of the intracellular action potential (IAP) profile due to elevation of the negative after-potentials could affect amplitude characteristics of surface EMG detected at any axial distance stronger than alteration in the neural drive. This was irrespective of the fact that the elevation of IAP negative after-potential was applied to fast fatigable motor units (MUs) only, while changes in frequency of activation (simulating neural drive changes) were applied to all MUs. In deeper muscles, where the fibre-electrode distance was larger, the peripheral effect was more pronounced. The normalization of EMG amplitude characteristics to an M-wave one could result only in partial elimination of peripheral factor influence CONCLUSIONS: The increase in RMS of surface EMG during the early gains in strength should not be directly related to the changes in the neural drive. The relatively small but long-lasting elevated free resting calcium after high-resistance strength training could result in force potentiation and EMG increase.

Predictive factors for complete pathological response in hormone receptor-negative breast cancer patients undergoing neoadjuvant chemotherapy.

Complete pathological response (pCR) is a pivotal predictor of enhanced disease-free and overall survival rates in breast cancer patients. Accurate prediction of pCR is therefore of paramount clinical significance. This retrospective study aimed to delineate the factors associated with pCR through a comprehensive analysis encompassing clinical, pathological, and immunohistochemical profiling of patients diagnosed with hormone receptor-negative invasive ductal carcinomas. The study cohort was composed of 73 female patients. The cases were reviewed retrospectively using data from University Hospital "Tsaritsa Yoanna" in Sofia, spanning the ten-year period from 2010 to 2020. Univariate analyses demonstrated that patients diagnosed with a higher disease stage, specifically stage IIIb, exhibited a notable association with an unfavorable response to neoadjuvant chemotherapy (NCT) [OR 4.5455 (95%CI 1.6810 - 12.2910); p = 0.0029]. Invasive carcinomas containing a ductal carcinoma in situ (DCIS) component [OR 0.3333 (95%CI 0.1226 - 0.9063); p = 0.0313] or were classified as poorly differentiated [OR 0.3056 (95%CI 0.1159 - 0.8055); p = 0.0165] demonstrated an enhanced likelihood of achieving pCR. Tumors expressing CD10 [OR 0.1452 (95%CI 0.0515 - 0.4093); p = 0.0003] and tumors lacking EGFR [OR 3.9722 (95%CI 1.4691 - 10.7399); p = 0.0066] exhibited a markedly elevated rate of pCR. Multivariate regression analysis supported findings. In conclusion, hormone receptor-negative breast tumors stand to benefit from increased pCR rates if they encompass a DCIS component and exhibit CD10 expression while lacking EGFR expression. These findings underscore the importance of comprehensive profiling in predicting pCR outcomes in hormone receptor-negative breast cancer patients undergoing neoadjuvant chemotherapy.

COVID-19 vaccination outcomes in patients with a solid malignancy: Insights from extensive real-world data and propensity score matched analyses.

OBJECTIVES: This nationwide, multicentric, retrospective analysis of 1,126,946 COVID-19 cases (March 2020-June 2022) aims to elucidate the impact of COVID-19 vaccination on mortality in patients with a sole solid malignancy. METHODS: Using data from the national digital medical record repository, outcomes were compared among fully vaccinated and nonvaccinated cohorts, factoring in gender, virus type, age, vaccination status, vaccine type, and cancer type. Logistic regression calculated odds ratios (OR) and their significance. RESULTS: Among 6,050 patients with both cancer and comorbidities, 1,797 had only solid malignancy. Vaccinated individuals in this group had reduced mortality rates, especially those >63 years (OR 0.169 [95% confidence interval [CI] 0.090-0.317]; P < .001). Lower deaths were observed in non-ICU (OR 0.193 [95% CI 0.097-0.382]; P < .001) and ICU cases (OR 0.224 [95% CI 0.077-0.646]; P = .003), with both vaccine types. No statistically significant benefits were observed against delta and omicron variants. Intrathoracic malignancies (OR 0.376 [95% CI 0.146-0.971]; P = .043) and palliative treatment (OR 0.384 [95% CI 0.192-0.766]; P = .006) showed vaccination benefits. Logistic regression revealed a higher fatal risk in nonvaccinated males >63. Propensity score matching supported these outcomes. CONCLUSIONS: Patients with sole solid malignancies face elevated COVID-19 mortality risk, particularly without active cytostatic therapy, with advanced disease on palliative treatment, or intrathoracic malignancies.

Nationwide analysis of the impact of COVID-19 in patients with a cardiovascular, oncological or chronic pulmonary disease in the context of an Eastern European country with a low vaccination rate, Bulgaria: March 2020-April 2022.

OBJECTIVE: This study focused on Bulgarian patient cohorts harbouring a single documented chronic comorbidity-cardiovascular pathology, an oncological disease or a chronic pulmonary diseases (CPD) comparing the outcomes in fully vaccinated and non-vaccinated populations classified by sex and age groups in ambulatory, hospital and intensive care unit (ICU) settings at the national level. DESIGN: Retrospective analysis SETTINGS, PARTICIPANTS AND OUTCOME MEASURES: In total, 1 126 946 patients with confirmed COVID-19, on a national level, were retrospectively analysed between March 2020 and April 2022, using data from the Ministry of Health's United Information Portal, launched in March 2020. RESULTS: Of all the confirmed 247 441 hospitalised cases of COVID-19, 67 723 (27.3%) had documented cardiovascular disease (CVD), 2140 (0.9%) had confirmed solid malignancy (regardless of stage) and 3243 (1.3%) had established CPD as their only chronic pathology. The number of cumulative deaths in each subgroup was 10 165 (in-hospital=5812 and ICU=4353); 4.0% vaccinated (410/10 165, p<0.001), 344 (in-hospital=196 and ICU=148), 4.9% vaccinated (17/344, p<0.001), 494 (in-hospital=287 and ICU=207) and 5.2% vaccinated (26/494, p<0.001), respectively. Statistical significance (p<0.001) was obtained in favour of reduced ambulatory, hospitalisation and both in-hospital and ICU-related mortality in the vaccinated cohorts, and BNT162b2 was the most effective at preventing mortality in all age groups. CONCLUSIONS: This retrospective analysis shows that patients vaccinated against COVID-19 demonstrated trends of reduced hospitalisations and premature mortality in patients with CVD, solid malignancy or CPD as a single comorbidity.

Early to sustained impacts of lethal radiation on circulating miRNAs in a minipig model.

Early diagnosis of lethal radiation is imperative since its intervention time windows are considerably short. Hence, ideal diagnostic candidates of radiation should be easily accessible, enable to inform about the stress history and objectively triage subjects in a time-efficient manner. Therefore, the small molecules such as metabolites and microRNAs (miRNAs) from plasma are legitimate biomarker candidate for lethal radiation. Our objectives were to comprehend the radiation-driven molecular pathogenesis and thereby determine biomarkers of translational potential. We investigated an established minipig model of LD70/45 total body irradiation (TBI). In this pilot study, plasma was collected pre-TBI and at multiple time points post-TBI. The majority of differentially expressed miRNAs and metabolites were perturbed immediately after TBI that potentially underlined the severity of its acute impact. The integrative network analysis of miRNA and metabolites showed a cohesive response; the early and consistent perturbations of networks were linked to cancer and the shift in musculoskeletal atrophy synchronized with the comorbidity-networks associated with inflammation and bioenergy synthesis. Subsequent comparative pipeline delivered 92 miRNAs, which demonstrated sequential homology between human and minipig, and potentially similar responses to lethal radiation across these two species. This panel promised to retrospectively inform the time since the radiation occurred; thereby could facilitate knowledge-driven interventions.

Identifying Stress-Exacerbated Thermal-Injury Induced MicroRNAs.

Using a model of combat and operational stress reaction (COSR), our lab recently showed that exposure to an unpredictable combat stress (UPCS) procedure prior to a thermal injury increases pain sensitivity in male rats. Additionally, our lab has recently shown that circulating extracellular vesicle-microRNAs (EV-miRNAs), which normally function to suppress inflammation, were downregulated in a male rat model of neuropathic pain. In this current study, male and female rats exposed to UPCS, followed by thermal injury, were evaluated for changes in circulating EV-miRNAs. Adult female and male Sprague Dawley rats were exposed to a UPCS procedure for either 2 or 4 weeks. Groups consisted of the following: nonstress (NS), stress (S), NS + thermal injury (TI), and S + TI. Mechanical sensitivity was measured, and plasma was collected at baseline, throughout the UPCS exposure, and post-thermal injury. EV-miRNA isolation was performed, followed by small RNA sequencing and subsequent data analysis. UPCS exposure alone resulted in mechanical allodynia in both male and female rats at specific time points. Thermal-injury induction occurring at peak UPCS resulted in increased mechanical allodynia in the injured hind paw compared to thermal injury alone. Differential expression of the EV-miRNAs was observed between the NS and S groups as well as between NS + TI and S + TI groups. Consistent differences in EV-miRNAs are detectable in both COSR as well as during the development of mechanical sensitivity and potentially serve as key regulators, biomarkers, and targets in the treatment of COSR and thermal-injury induced mechanical sensitivity. PERSPECTIVE: This article presents the effects of unpredictable combat stress and thermal injury on EV-contained microRNAs in an animal model. These same mechanisms may exist in clinical patients and could be future prognostic and diagnostic biomarkers.

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.

Gene-metabolite networks associated with impediment of bone fracture repair in spaceflight.

Adverse effects of spaceflight on musculoskeletal health increase the risk of bone injury and impairment of fracture healing. Its yet elusive molecular comprehension warrants immediate attention, since space travel is becoming more frequent. Here we examined the effects of spaceflight on bone fracture healing using a 2 mm femoral segmental bone defect (SBD) model. Forty, 9-week-old, male C57BL/6J mice were randomized into 4 groups: 1) Sham surgery on Ground (G-Sham); 2) Sham surgery housed in Spaceflight (FLT-Sham); 3) SBD surgery on Ground (G-Surgery); and 4) SBD surgery housed in Spaceflight (FLT-Surgery). Surgery procedures occurred 4 days prior to launch; post-launch, the spaceflight mice were house in the rodent habitats on the International Space Station (ISS) for approximately 4 weeks before euthanasia. Mice remaining on the Earth were subjected to identical housing and experimental conditions. The right femur from half of the spaceflight and ground groups was investigated by micro-computed tomography (µCT). In the remaining mice, the callus regions from surgery groups and corresponding femoral segments in sham mice were probed by global transcriptomic and metabolomic assays. µCT confirmed escalated bone loss in FLT-Sham compared to G-Sham mice. Comparing to their respective on-ground counterparts, the morbidity gene-network signal was inhibited in sham spaceflight mice but activated in the spaceflight callus. µCT analyses of spaceflight callus revealed increased trabecular spacing and decreased trabecular connectivity. Activated apoptotic signals in spaceflight callus were synchronized with inhibited cell migration signals that potentially hindered the wound site to recruit growth factors. A major pro-apoptotic and anti-migration gene network, namely the RANK-NFκB axis, emerged as the central node in spaceflight callus. Concluding, spaceflight suppressed a unique biomolecular mechanism in callus tissue to facilitate a failed regeneration, which merits a customized intervention strategy.

Influence of motor unit synchronization on amplitude characteristics of surface and intramuscularly recorded EMG signals.

The increase in muscle strength without noticeable hypertrophic adaptations is very important in some sports. Motor unit (MU) synchronisation and higher rate of MU activation are proposed as possible mechanisms for such a strength and electromyogram (EMG) increase in the early phase of a training regimen. Root mean square and/or integrated EMG are amplitude measures commonly used to estimate the adaptive changes in efferent neural drive. EMG amplitude characteristics could change also because of alteration in intracellular action potential (IAP) spatial profile. We simulated MUs synchronization under different length of the IAP profile. Different synchronization was simulated by variation of the percent of discharges in a referent MU, to which a variable percent of remaining MUs was synchronized. Population synchrony index estimated the degree of MU synchronization in EMG signals. We demonstrate that the increase in amplitude characteristics due to MU synchronization is stronger in surface than in intramuscularly detected EMG signals. However, the effect of IAP profile lengthening on surface detected EMG signals could be much stronger than that of MU synchronization. Thus, changes in amplitude characteristics of surface detected EMG signals with progressive strength training could hardly be used as an indicator of changes in neural drive without testing possible changes in IAPs.

microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation.

Lethal total body irradiation (TBI) triggers multifactorial health issues in a potentially short time frame. Hence, early signatures of TBI would be of great clinical value. Our study aimed to interrogate microRNA (miRNA) and metabolites, two biomolecules available in blood serum, in order to comprehend the immediate impacts of TBI. Mice were exposed to a lethal dose (9.75 Gy) of Cobalt-60 gamma radiation and euthanized at four time points, namely, days 1, 3, 7 and 9 post-TBI. Serum miRNA libraries were sequenced using the Illumina small RNA sequencing protocol, and metabolites were screened using a mass spectrometer. The degree of early impacts of irradiation was underscored by the large number of miRNAs and metabolites that became significantly expressed during the Early phase (day 0 and 1 post-TBI). Radiation-induced inflammatory markers for bone marrow aplasia and pro-sepsis markers showed early elevation with longitudinal increment. Functional analysis integrating miRNA-protein-metabolites revealed inflammation as the overarching host response to lethal TBI. Early activation of the network linked to the synthesis of reactive oxygen species was associated with the escalated regulation of the fatty acid metabolism network. In conclusion, we assembled a list of time-informed critical markers and mechanisms of significant translational potential in the context of a radiation exposure event.

Gene-Metabolite Network Linked to Inhibited Bioenergetics in Association With Spaceflight-Induced Loss of Male Mouse Quadriceps Muscle.

Prolonged residence of mice in spaceflight is a scientifically robust and ethically ratified model of muscle atrophy caused by continued unloading. Under the Rodent Research Program of the National Aeronautics and Space Administration (NASA), we assayed the large-scale mRNA and metabolomic perturbations in the quadriceps of C57BL/6j male mice that lived in spaceflight (FLT) or on the ground (control or CTR) for approximately 4 weeks. The wet weights of the quadriceps were significantly reduced in FLT mice. Next-generation sequencing and untargeted mass spectroscopic assays interrogated the gene-metabolite landscape of the quadriceps. A majority of top-ranked differentially suppressed genes in FLT encoded proteins from the myosin or troponin families, suggesting sarcomere alterations in space. Significantly enriched gene-metabolite networks were found linked to sarcomeric integrity, immune fitness, and oxidative stress response; all inhibited in space as per in silico prediction. A significant loss of mitochondrial DNA copy numbers in FLT mice underlined the energy deprivation associated with spaceflight-induced stress. This hypothesis was reinforced by the transcriptomic sequencing-metabolomics integrative analysis that showed inhibited networks related to protein, lipid, and carbohydrate metabolism, and adenosine triphosphate (ATP) synthesis and hydrolysis. Finally, we discovered important upstream regulators, which could be targeted for next-generation therapeutic intervention for chronic disuse of the musculoskeletal system. © 2020 The Authors. Journal of Bone and Mineral Research published by American Society for Bone and Mineral Research.

Identifying Plasma Derived Extracellular Vesicle (EV) Contained Biomarkers in the Development of Chronic Neuropathic Pain.

Research into potentially novel biomarkers for chronic pain development is lacking. microRNAs (miRNAs) are attractive candidates as biomarkers due to their conservation across species, stability in liquid biopsies, and variation that corresponds to a pathologic state. miRNAs can be sorted into extracellular vesicles (EVs) within the cell and released from the site of injury. EVs transfer cargo molecules between cells thus affecting key intercellular signaling pathways. The focus of this study was to determine the plasma derived EV miRNA content in a chronic neuropathic pain rat model. This was accomplished by performing either spinal nerve ligation (SNL; n = 6) or sham (n = 6) surgery on anesthetized male Sprague-Dawley rats. Mechanosensitivity was assessed and plasma derived EV RNA was isolated at baseline (BL), day 3, and 15 postnerve injury. EV extracted small RNA was sequenced followed by differentially expressed (DE) miRNAs and gene target enrichment/signaling pathway analysis performed using R packages and TargetScan/Ingenuity pathway analysis (IPA), respectively. Seven of the DE miRNAs were validated by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR). The data indicated that SNL rats displayed a time-dependent threshold reduction in response to evoked stimuli from day 3 to day 15 postnerve injury. The data also revealed that 22 and 74 miRNAs at day 3 and 15, respectively, and 33 miRNAs at both day 3 and 15 were uniquely DE between the SNL and sham groups. The key findings from this proposal include (1) the majority of the DE EV miRNAs, which normally function to suppress inflammation, were downregulated, and (2) several of the plasma derived DE EV miRNAs reflect previously observed changes in the injured L5 nerve. The plasma derived DE EV miRNAs regulate processes important in the development and maintenance of neuropathic pain states and potentially serve as key regulators, biomarkers, and targets in the progression and treatment of chronic neuropathic pain. PERSPECTIVE: This article describes the DE miRNA content of plasma derived EVs, comparing neuropathic pain to normal conditions. This data indicates that EV miRNAs may be important in nociception and may also serve as biomarkers for chronic pain. These results encourage further research on EV miRNAs in chronic neuropathic pain sufferers.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.

Contributions of polyunsaturated fatty acids (PUFA) on cerebral neurobiology: an integrated omics approach with epigenomic focus.

The epigenetic landscape is vulnerable to diets. Here, we investigated the influence of different polyunsaturated fatty acids (PUFA) dietary supplements on rodents' nervous system development and functions and potential consequences to neurodegenerative disorders. Our previous nutrigenomics study showed significant impact of high n-3 PUFA-enriched diet (ERD) on synaptogenesis and various neuromodulators. The present study introduced a second equicaloric diet with n-6 PUFA balanced by n-3 PUFA (BLD). The typical lab diet with high n-6 PUFA was the baseline. Transcriptomic and epigenetic investigations, namely microRNA (miRNA) and DNA methylation assays, were carried out on the hemibrains of the C57BL/6j mice fed on any of these three diets from their neonatal age to midlife. Integrating the multiomics data, we focused on the genes encoding both hypermethylated CpG islands and suppressed transcripts. In addition, miRNA:mRNA pairs were screened to identify those overexpressed miRNAs that reduced transcriptional expressions. The majority of miRNAs overexpressed by BLD are associated with Alzheimer's and schizophrenia. BLD implicated long-term potentiation, memory, cognition and learning, primarily via hypermethylation of those genes that enrich the calcium-releasing neurotransmitters. ERD caused hypermethylation of those genes that enrich cytoskeletal development networks and promote the formation of neuronal precursors. We drew the present observations in light of our limited knowledge regarding the epigenetic influences on biofunctions. A more comprehensive study is essential to understand the broad influences of dietary supplements and to suggest optimal dietary solutions for neurological disorders.

Muscle fatigue during dynamic contractions assessed by new spectral indices.

PURPOSE: The aim of the present study was to test the applicability and sensitivity of new electromyography (EMG) spectral indices in assessing peripheral muscle fatigue during dynamic knee-extension exercise. METHODS: Seven subjects completed 10 sets of 15 repetitions of right knee-extension exercise lifting 50% of their one-repetition maximum. Torque (T), knee-joint angle, and the interference EMG of rectus femoris muscle were recorded simultaneously. Maximal voluntary isometric contraction (MVC) was tested before and after exercise. Median spectral frequency (Fmed) and new spectral indices of muscle fatigue (FInsmk) were calculated for each repetition. RESULTS: The rate and range of FInsmk- and Fmed-relative changes against the first repetition of the corresponding set increased gradually across successive repetitions within the set, reflecting accumulation of peripheral muscle fatigue. The maximal change of FInsmk observed in the present experiment was approximately eightfold, whereas that of Fmed was only 32%. Significant between-subject variability in the range of FInsmk changes (P < 0.0001) was found, so a hierarchical cluster analysis of muscle fatigue indices was conducted. Three distinct subgroups of subjects were identified: high (N = 1, FInsmk change > 400%), medium (N = 4, 200% < FInsmk change < 400%), and low (N = 2, FInsmk change < 200%) muscle fatigability. The changes in muscle performance during (last vs first repetition peak T, P = 0.03) and after (post- vs preexercise MVC, P = 0.012) exercise were significantly different between clusters (one-way ANOVA). The rate of fatigue development was also significantly different between clusters (linear regression analysis of Fmed and FInsmk changes). CONCLUSIONS: The new spectral indices are a valid and reliable tool for assessment of muscle fatigability irrespective of EMG signal variability caused by dynamic muscle contractions, and these indices are more sensitive than those traditionally used.