Protein-Protein Interactions (PPI) via Deep Neural Network (DNN)

Entering the 21st century, computer science and biological research have entered a stage of rapid development. With the rapid inflow of capital into the field of significant health research, a large number of scholars and investors have begun to focus on the impact of neural network science on biometrics, especially the study of biological interactions. With the rapid development of computer technology, scientists improve or perfect traditional experimental methods. This chapter aims to prove the reliability of the methodology and computing algorithms developed by Satyajit Mahapatra and Ivek Raj Gupta's project team. In this chapter, three datasets take the responsibility to testify the computing algorithms, and they are S. cerevisiae, H. pylori, and Human-B. Anthracis. Among these three sets of data, the S. cerevisiae is the core subset. The result shows 87%, 87.5%, and 89% accuracy and 87%, 86%, and 87% precision for these three data sets, respectively.

Effects of Epidermal Growth Factor and Myo-Inositol on Nuclear Configuration and Subsequent Embryonic Development of Sheep Oocytes

Growth factors and vitamin-like substances have great positive importance in most biological interactions in the cellular level. The addition of these elements in the culture media will increase the yield of the resulting embryos and improve quality. We examined the effects of epidermal growth factor (EGF) and myo-inositol (MI) on meiotic maturation and yields of blastocyst of Awassi sheep oocyte across two experiments. The oocytes obtained were subjected into three treatments: A (without EGF nor MI), B (10 ng/ml EGF + 20 mmol/l MI) and C (50 ng/ml EGF +40 mmol/l MI). Oocytes were then cultured in Ham's F-10 medium supplemented with 5% (v: v) fetal calf serum and 40 ng/ml follicle - stimulating hormone. In the first experiment, during the 27-h culture period, the oocytes were assessed for germinal vesicle break down, metaphase-I and metaphase-II stages across three-time intervals (9, 21 and 27-h). Results of the experiment showed that EGF and MI enhanced the rates of germinal vesicle break down phase (1.53%; 27-h interval; lowest value), metaphase-I (33.87%; 21-h interval) and metaphase-II (89.23%; 27-h interval). In the second experiment, the oocytes incubated in treatment B achieved the highest rates of cleavage (81.96%), 2-8 cell (62.35%) and blastocyst (45.09%). It is concluded from the present study that incubating sheep oocytes in culture media containing a cocktail of EGF (10 ng/ml) and MI (20 mmol/l) significantly improves the rates of metaphase-II, fertilization and blastocyst rates.

Pancreatic Cancer Patient-Derived Organoid Platforms: A Clinical Tool to Study Cell- and Non-Cell-Autonomous Mechanisms of Treatment Response

For many years, cell lines and animal models have been essential to improve our understanding of the basis of cell metabolism, signaling, and genetics. They also provided an essential boost to cancer drug discovery. Nevertheless, these model systems failed to reproduce the tumor heterogeneity and the complex biological interactions between cancer cells and human hosts, making a high priority search for alternative methods that are able to export results from model systems to humans, which has become a major bottleneck in the drug development. The emergent human in vitro 3D cell culture technologies have attracted widespread attention because they seem to have the potential to overcome these limitations. Organoids are unique 3D culture models with the ability to self-organize in contained structures. Their versatility has offered an exceptional window of opportunity to approach human cancers. Pancreatic cancers (PCs) patient-derived-organoids (PDOs) preserve histological, genomic, and molecular features of neoplasms they originate from and therefore retain their heterogeneity. Patient-derived organoids can be established with a high success rate from minimal tissue core specimens acquired with endoscopic-ultrasound-guided techniques and assembled into platforms, representing tens to hundreds of cancers each conserving specific features, expanding the types of patient samples that can be propagated and analyzed in the laboratory. Because of their nature, PDO platforms are multipurpose systems that can be easily adapted in co-culture settings to perform a wide spectrum of studies, ranging from drug discovery to immune response evaluation to tumor-stroma interaction. This possibility to increase the complexity of organoids creating a hybrid culture with non-epithelial cells increases the interest in organoid-based platforms giving a pragmatic way to deeply study biological interactions in vitro. In this view, implementing organoid models in co-clinical trials to compare drug responses may represent the next step toward even more personalized medicine. In the present review, we discuss how PDO platforms are shaping modern-day oncology aiding to unravel the most complex aspects of PC.

RECORD OF Ostrea puelchana D’ORBIGNY, 1842 (BIVALVIA: OSTREIDAE), AS NEW EPIBIONT IN Eriphia gonagra (FABRICIUS, 1781) (CRUSTACEA: ERIPHIIDAE) FROM NORTHEASTERN BRAZIL

In this paper, we describe the first association of the ostreid species Ostrea puelchana d’Orbigny, 1842, as new epibiont in Eriphia gonagra (Fabricius, 1781), with material collected in Northeastern Brazil. The specimens of E. gonagra were collected manually in November of 2020 during the low tide in the Barra de Catuama beach, State of Pernambuco. Among 10 specimens collected, only one adult male showed the presence of two commensal specimens of O. puelchana adhered in the epibranchial and antero-lateral regions of the basibiont (right side). The presence of the epibiont O. puelchana on the new host E. gonagra expands the range of the crustacean species potentially used as hosts by this oyster along the Brazilian coast. Keywords: marine invertebrates, biological interactions, Pernambuco, commensalism, beachrocks.

Characterisation of a Novel Benzopyran Library Using High-Throughput Microscopy

<p>Drug discovery is a multi-disciplinary field incorporating both chemistry and biology to create novel pharmaceuticals. Nature synthesizes a diverse range of chemical entities that can demonstrate a wide range of biological interactions, though often produces these compounds in small amounts. Using natures structural diversity as a template, organic synthetic chemistry can tap into the structures of natural products and provide novel structures as well as overcome supply issues through large-scale synthetic chemical processes. A novel benzopyran library was synthesised by Sandile Simelane by reacting 3,4,6,-tri-O-acetyl-D-galactal with various phenols to create a novel focused library of bridged benzopyrans. Each molecule has unique functional groups at defined points in the structure due to varying the functional groups on the phenol, allowing for variation within the library whilst retaining the core scaffold. In this thesis, the bioactivity of this novel benzopyran library was explored using a phenotypic screen measuring growth inhibition. A compound, S13, was determined to be the most potent in the library, therefore genome-wide screening was performed using S13. High-throughput microscopy of 4,100 strains, each with a different GFP-tagged protein, was utilized to determine proteins that increased in abundance or changed localization in response to perturbation with S13. Following treatment with S13, the yeast vacuole increased in size due to an aggregation of proteins in the vacuolar lumen. The increase in vacuole size was coincident with a decrease in vacuolar acidity, potentially disrupted autophagy and the upregulation of several proteins involved in ergosterol biosynthesis. Together, these results reveal a novel bridged benzopyran that increases vacuolar size and pH through an epistatic mechanism involving ergosterol biosynthesis.</p>

Characterisation of a Novel Benzopyran Library Using High-Throughput Microscopy

<p>Drug discovery is a multi-disciplinary field incorporating both chemistry and biology to create novel pharmaceuticals. Nature synthesizes a diverse range of chemical entities that can demonstrate a wide range of biological interactions, though often produces these compounds in small amounts. Using natures structural diversity as a template, organic synthetic chemistry can tap into the structures of natural products and provide novel structures as well as overcome supply issues through large-scale synthetic chemical processes. A novel benzopyran library was synthesised by Sandile Simelane by reacting 3,4,6,-tri-O-acetyl-D-galactal with various phenols to create a novel focused library of bridged benzopyrans. Each molecule has unique functional groups at defined points in the structure due to varying the functional groups on the phenol, allowing for variation within the library whilst retaining the core scaffold. In this thesis, the bioactivity of this novel benzopyran library was explored using a phenotypic screen measuring growth inhibition. A compound, S13, was determined to be the most potent in the library, therefore genome-wide screening was performed using S13. High-throughput microscopy of 4,100 strains, each with a different GFP-tagged protein, was utilized to determine proteins that increased in abundance or changed localization in response to perturbation with S13. Following treatment with S13, the yeast vacuole increased in size due to an aggregation of proteins in the vacuolar lumen. The increase in vacuole size was coincident with a decrease in vacuolar acidity, potentially disrupted autophagy and the upregulation of several proteins involved in ergosterol biosynthesis. Together, these results reveal a novel bridged benzopyran that increases vacuolar size and pH through an epistatic mechanism involving ergosterol biosynthesis.</p>

Role of the Microbiome in Regulating Bone Metabolism and Susceptibility to Osteoporosis

The human microbiota functions at the interface between diet, medication-use, lifestyle, host immune development and health. It is therefore closely aligned with many of the recognised modifiable factors that influence bone mass accrual in the young, and bone maintenance and skeletal decline in older populations. While understanding of the relationship between micro-organisms and bone health is still in its infancy, two decades of broader microbiome research and discovery supports a role of the human gut microbiome in the regulation of bone metabolism and pathogenesis of osteoporosis as well as its prevention and treatment. Pre-clinical research has demonstrated biological interactions between the microbiome and bone metabolism. Furthermore, observational studies and randomized clinical trials have indicated that therapeutic manipulation of the microbiota by oral administration of probiotics may influence bone turnover and prevent bone loss in humans. In this paper, we summarize the content, discussion and conclusions of a workshop held by the Osteoporosis and Bone Research Academy of the Royal Osteoporosis Society in October, 2020. We provide a detailed review of the literature examining the relationship between the microbiota and bone health in animal models and in humans, as well as formulating the agenda for key research priorities required to advance this field. We also underscore the potential pitfalls in this research field that should be avoided and provide methodological recommendations to facilitate bridging the gap from promising concept to a potential cause and intervention target for osteoporosis.

Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics

Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial warfare comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeast Saccharomyces cerevisiae, expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory's prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.

Physical and biological constraints on the capacity for life-history expression of anadromous salmonids: an Eel River, California, case study

Recovery of anadromous salmonid populations is complicated by their complex life-histories. We examined the spatiotemporal interplay of stream temperature, geomorphic features, and a species’ thermal sensitivity mediated by biological interactions in a case study of steelhead trout (Oncorhynchus mykiss) and Chinook salmon (O. tshawytscha) in California’s Eel River watershed. We estimated habitat suitability and fish capacity for each salmonid run and freshwater life stage during average, cool, and warm years in each of the watershed’s subbasins, including a historically-occupied high-elevation subbasin upstream of an impassable dam. Our estimates varied depending on whether we accounted for exposure to the Sacramento pikeminnow (Ptychocheilus grandis), an introduced predator/competitor. Our results indicate that the dammed subbasin has substantial salmonid capacity relative to the rest of the watershed and could provide an important cool-water refuge during warm years and from pikeminnow, potentially improving the productivity and resilience of multiple anadromous salmonid populations. Our approach can be applied in any setting where spatially explicit habitat metrics can be estimated and population specific and life-stage specific habitat criteria can be specified.