How Not To Drown in Data:A Guide for Biomaterial Engineers

High-throughput assays that produce hundreds of measurements per sample are powerful tools for quantifying cell–material interactions. With advances in automation and miniaturization in material fabrication, hundreds of biomaterial samples can be rapidly produced, which can then be characterized using these assays. However, the resulting deluge of data can be overwhelming. To the rescue are computational methods that are well suited to these problems. Machine learning techniques provide a vast array of tools to make predictions about cell–material interactions and to find patterns in cellular responses. Computational simulations allow researchers to pose and test hypotheses and perform experiments in silico. This review describes approaches from these two domains that can be brought to bear on the problem of analyzing biomaterial screening data

Atherogenesis

This monograph will bring out the state-of-the-art advances in the dynamics of cholesterol transport and will address several important issues that pertain to oxidative stress and inflammation. The book is divided into three major sections. The book will offer insights into the roles of specific cytokines, inflammation, and oxidative stress in atherosclerosis and is intended for new researchers who are curious about atherosclerosis as well as for established senior researchers and clinicians who would be interested in novel findings that may link various aspects of the disease

Characterization of antimicrobial peptides deriving from insects and their application in the biomedical field

Antibiotics are the current drugs used to treat pathogenic bacteria, but their prolonged use contributes to the development and spread of drug-resistant microorganisms. The antibiotic resistance issue led to the need to find new alternative molecules, which should be less prone to bacterial resistance. Antimicrobial peptides (AMPs) aroused great interest as potential next-generation antibiotics. AMPs are involved in several defence-related processes such as the binding and neutralization of endotoxins, the modulation of the immune responses to infection and the killing of pathogens. Antimicrobial peptides are small molecules with an amino acid composition ranging from 10 to 100 residues and are biosynthesized by all living organisms but it is known that the class of insects represents the largest source of these molecules. This aspect is related to insect’s biodiversity and their ability to live in hostile environments rich of pathogens. Most insect AMPs are cationic molecules due to the presence of basic residues and according to their amino acid sequences and structures, they can be classified in four different groups: cysteine-rich peptides (e.g., defensins), the α-helical peptides (e.g., cecropins), glycine-rich proteins (e.g., attacins) and proline-rich peptides (e.g., drosocins). Insect AMPs have demonstrated to be useful in several applications concerning the pharmaceutical as well as the agricultural fields. Moreover, insect AMPs aroused great interest for their biomedical application thanks to the increasing number of peptides that can inhibit human pathogens. For this reason, this Ph.D. project aimed to the identification of antimicrobial peptides deriving from insects, particularly from the Black Soldier Fly Hermetia illucens (L.) (Diptera: Stratiomyidae). Through a combination of transcriptomics and bioinformatics analysis, 57 antimicrobial peptides have been identified from H. illucens insect. Through an in silico analysis, the biological activity have been predicted and the physio-chemical properties have been calculated for all the identified peptides. Based on the bioinformatics results, the in vitro production of the most promising sequences has been performed through molecular cloning strategies in order to evaluate the antibacterial activity in vitro. Particularly, some of the identified peptides (C16571, C46948, C16634, and C7985) showed the ability to inhibit E. coli growth at a concentration value of 3 μM. For the C15867 peptide, recombinantly produced and expressed, a MIC (Minimum Inhibitory Concentration) value of 18 μM has been determined. Moreover, an in vivo approach was carried out for the identification of antimicrobial peptides by extracting the hemolymph from the H. illucens larvae, recovering then the peptides fraction from the larvae’s plasma and its antibacterial activity has been evaluated against both Gram-positive and Gram-negative bacteria. The performed analysis showed that a small amount (7.5/15 μL) of the peptide fraction recovered from the larvae’s plasma was able to inhibit the cell growth of different bacterial strains

Psr1p interacts with SUN/sad1p and EB1/mal3p to establish the bipolar spindle

Regular Abstracts - Sunday Poster Presentations: no. 382During mitosis, interpolar microtubules from two spindle pole bodies (SPBs) interdigitate to create an antiparallel microtubule array for accommodating numerous regulatory proteins. Among these proteins, the kinesin-5 cut7p/Eg5 is the key player responsible for sliding apart antiparallel microtubules and thus helps in establishing the bipolar spindle. At the onset of mitosis, two SPBs are adjacent to one another with most microtubules running nearly parallel toward the nuclear envelope, creating an unfavorable microtubule configuration for the kinesin-5 kinesins. Therefore, how the cell organizes the antiparallel microtubule array in the first place at mitotic onset remains enigmatic. Here, we show that a novel protein psrp1p localizes to the SPB and plays a key role in organizing the antiparallel microtubule array. The absence of psr1+ leads to a transient monopolar spindle and massive chromosome loss. Further functional characterization demonstrates that psr1p is recruited to the SPB through interaction with the conserved SUN protein sad1p and that psr1p physically interacts with the conserved microtubule plus tip protein mal3p/EB1. These results suggest a model that psr1p serves as a linking protein between sad1p/SUN and mal3p/EB1 to allow microtubule plus ends to be coupled to the SPBs for organization of an antiparallel microtubule array. Thus, we conclude that psr1p is involved in organizing the antiparallel microtubule array in the first place at mitosis onset by interaction with SUN/sad1p and EB1/mal3p, thereby establishing the bipolar spindle.postprin

Removal of antagonistic spindle forces can rescue metaphase spindle length and reduce chromosome segregation defects

Regular Abstracts - Tuesday Poster Presentations: no. 1925Metaphase describes a phase of mitosis where chromosomes are attached and oriented on the bipolar spindle for subsequent segregation at anaphase. In diverse cell types, the metaphase spindle is maintained at a relatively constant length. Metaphase spindle length is proposed to be regulated by a balance of pushing and pulling forces generated by distinct sets of spindle microtubules and their interactions with motors and microtubule-associated proteins (MAPs). Spindle length appears important for chromosome segregation fidelity, as cells with shorter or longer than normal metaphase spindles, generated through deletion or inhibition of individual mitotic motors or MAPs, showed chromosome segregation defects. To test the force balance model of spindle length control and its effect on chromosome segregation, we applied fast microfluidic temperature-control with live-cell imaging to monitor the effect of switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. We show that spindle midzone proteins kinesin-5 cut7p and microtubule bundler ase1p contribute to outward pushing forces, and spindle kinetochore proteins kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Our results stress the importance of proper chromosome-to-microtubule attachment over spindle length regulation for proper chromosome segregation.postprin

New Insights on Biofilm Antimicrobial Strategies

Over the last few decades, the study of microbial biofilms has been gaining interest among the scientific community. These microbial communities comprise cells adhered to surfaces that are surrounded by a self-produced exopolymeric matrix that protects biofilm cells against different external stresses. Biofilms can have a negative impact on different sectors within society, namely in agriculture, food industries, and veterinary and human health. As a consequence of their metabolic state and matrix protection, biofilm cells are very difficult to tackle with antibiotics or chemical disinfectants. Due to this problem, recent advances in the development of antibiotic alternatives or complementary strategies to prevent or control biofilms have been reported. This book includes different strategies to prevent biofilm formation or to control biofilm development and includes full research articles, reviews, a communication, and a perspective

Additional file 2 of Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice

Details of ordinary differential equation solution and synthetic data generation. (PDF 149 kb