Unraveling the Differences of the Hydrolytic Activity of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase: A Quantum Mechanics–Molecular Mechanics Modeling Study

Chagas’ disease, also known as American trypanosomiasis, is a lethal, chronic disease that currently affects more than 10 million people in Central and South America. The trans-sialidase from Trypanosoma cruzi (T. cruzi, TcTS) is a crucial enzyme for the survival of this parasite: sialic acids from the host are transferred to the cell surface glycoproteins of the trypanosome, thereby evading the host’s immune system. On the other hand, the sialidase of T. rangeli (TrSA), which shares 70% sequence identity with TcTS, is a strict hydrolase and shows no trans-sialidase activity. Therefore, TcTS and TrSA represent an excellent framework to understand how different catalytic activities can be achieved with extremely similar structures. By means of combined quantum mechanics–molecular mechanics (QM/MM, SCC-DFTB/Amberff99SB) calculations and umbrella sampling simulations, we investigated the hydrolysis mechanisms of TcTS and TrSA and computed the free energy profiles of these reactions. The results, together with our previous computational investigations, are able to explain the catalytic mechanism of sialidases and describe how subtle differences in the active site make TrSA a strict hydrolase and TcTS a more efficient trans-sialidase.Fil: Bueren Calabuig, Juan A.. University of Florida; Estados UnidosFil: Pierdominici Sottile, Gustavo. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados Unido

Consumer attitudes and preference exploration towards fresh-cut salads using best–worst scaling and latent class analysis

This research explored the preferences and buying habits of a sample of 620 consumers of fresh-cut, ready-to-eat salads. A best–worst scaling approach was used to measure the level of preference stated by individuals regarding 12 attributes for quality (intrinsic, extrinsic and credence) of fresh-cut salads. The experiment was carried out through direct interviews at several large-scale retail outlets in the Turin metropolitan area (north-west of Italy). Out of the total number of questioned consumers, 35% said they did not consume fresh-cut salads. On the contrary, the rest of the involved sample expressed the highest degree of preference towards the freshness/appearance attribute, followed by the expiration date and the brand. On the contrary, attributes such as price, organic certification and food safety did not emerge as discriminating factors in consumer choices. Additionally, five clusters of consumers were identified, whose preferences are related both to purchasing styles and socio-demographic variables. In conclusion, this research has highlighted the positive attitude of consumers towards quality products backed by a brand, providing ideas for companies to improve within this sector and implement strategies to answer the needs of a new segment of consumers, by determining market opportunities that aim to strengthen local brands

In vitro osteogenic differentiation of human ES cells

Since their isolation in 1998, human embryonic stem (hES) cells have been shown to be capable of adopting various cell fates in vitro. Here, we present in vitro data demonstrating the directed commitment of human embryonic stem cells to the osteogenic lineage. Human ES cells are shown to respond to factors that promote osteogenesis, leading to activation of the osteogenic markers osteocalcin, parathyroid hormone receptor, bone sialoprotein, osteopontin, cbfa1, and collagen 1. Moreover, the mineralized nodules obtained are composed of hydroxyapatite, further establishing the similarity of osteoblasts in culture to bone. These results show that osteoblasts can be derived from human ES cultures in vitro and provide the basis for comparison of adult and embryonic-derived osteogenesis, and for an investigation of potential applications for hES cells in orthopaedic tissue repair

A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

Coat color is one of the most important phenotypic features in livestock breeds. Cinisara is a local cattle breed generally of uniform black color which occasionally presents a particular phenotype, with animals typically display a white band along their spine, from the head to the tail, and on the ventral line (color sidedness). Therefore, this breed provides an ideal model to study the genetic components underlying phenotypic variation in coat color. A total of 63 animals, ten with sidedness phenotype and 53 with uniform black color were genotyped with Illumina Bovine 50 K. The comparison among genome-wide association study and FST analysis revealed a single nucleotide polymorphism (SNP), ARS-BFGL-NGS-55928, significantly associated with the trait. Only one gene (PLK2)was annotated near the associated SNP in a window of ±200 kb. The protein encoded by this gene is a member of the polo-like kinases, the same family of several known coat-color candidate genes. Based on the reported results, we draw the possible conclusion that the identified marker is potentially associated with the coat color sidedness in Cinisara. The local breeds with their genetic variability represent an important resource and model to study the genetic basis affecting peculiar traits. Future studies would be particularly relevant to refine these results and to better understand the genetic basis for this phenotype

Exposure to the ROCK inhibitor fasudil promotes gliogenesis of neural stem cells in vitro

Fasudil is a clinically approved Rho-associated protein kinase (ROCK) inhibitor that has been used widely to treat cerebral consequences of subarachnoid hemorrhage. It is known to have a positive effect on animal models of neurological disorders including Parkinson's disease and stroke. However, its cellular effect on progenitor populations and differentiation is not clearly understood. While recent studies suggest that fasudil promotes the mobilization of neural stem cells (NSCs) from the subventricular zone in vivo and promotes the differentiation of the C17.2 cerebellar neuroprogenitor line in vitro, it is unclear whether fasudil is involved in the differentiation of primary NSCs. Here, we tested the effect of fasudil on mouse NSCs in vitro, and observed increased gliogenesis in NSCs derived from lateral ventricles. Upon treatment, fasudil promoted characteristics of neurogenesis including phenotypic changes in neural outgrowth and interkinetic nuclear-like movements as an immediate response, while Sox2 expression was maintained and GFAP expression increased. Moreover, the gliogenic response to fasudil medium was observed in both early postnatal and adult NSC cultures. Taken together, our results show that fasudil promotes the differentiation of NSCs into astroglial lineage, suggesting that it could be used to develop novel vitro gliogenesis models and regulate differentiation for neural repair

Expression of a SOX1 overlapping transcript in neural differentiation and cancer models

SOX1 is a member of the SOXB1 subgroup of transcription factors involved in early embryogenesis, CNS development and maintenance of neural stem cells. The structure and regulation of the human SOX1 locus has been less studied than that of SOX2, another member of the SOXB1 subgroup for which an overlapping transcript has been reported. Here we report that the SOX1 locus harbours a SOX1 overlapping transcript (SOX1-OT), and describe expression, splicing variants and detection of SOX1-OT in different stem and cancer cells. RT-PCR and RACE experiments were performed to detect and characterise the structure of SOX1-OT in neuroprogenitor cultures and across different cancer cell lines. SOX1-OT was found to present a complex structure including several unannotated exons, different transcript variants and at least two potential transcription start sites. SOX1-OT was found to be highly expressed in differentiated neural stem cells across different time points of differentiation, and its expression correlated with SOX1 gene expression. Concomitant expression of SOX1 and SOX1-OT was further observed in several cancer cell models. While the function of this transcript is unknown, the regulatory role reported for other lncRNAs strongly suggests a possible role for SOX1-OT in regulating SOX1 expression, as previously observed for SOX2. The elucidation of the genetic and regulatory context governing SOX1 expression will contribute to clarifying its role in stem cell differentiation and tumorigenesis

Impact of serum source on human mesenchymal stem cell osteogenic differentiation in culture

Human mesenchymal stem cells (MSCs) show promise for musculoskeletal repair applications. Animal-derived serum is extensively used for MSC culture as a source of nutrients, extracellular matrix proteins and growth factors. However, the routine use of fetal calf serum (FCS) is not innocuous due to its animal antigens and ill-defined composition, driving the development of alternatives protocols. The present study sought to reduce exposure to FCS via the transient use of human serum. Transient exposure to animal serum had previously proved successful for the osteogenic differentiation of MSCs but had not yet been tested with alternative serum sources. Here, human serum was used to support the proliferation of MSCs, which retained surface marker expression and presented higher alkaline phosphatase activity than those in FCS-based medium. Addition of osteogenic supplements supported strong mineralisation over a 3-week treatment. When limiting serum exposure to the first five days of treatment, MSCs achieved higher differentiation with human serum than with FCS. Finally, human serum analysis revealed significantly higher levels of osteogenic components such as alkaline phosphatase and 25-Hydroxyvitamin D, consistent with the enhanced osteogenic effect. These results indicate that human serum used at the start of the culture offers an efficient replacement for continuous FCS treatment and could enable short-term exposure to patient-derived serum in the future

Symmetry groups, semidefinite programs, and sums of squares

We investigate the representation of symmetric polynomials as a sum of squares. Since this task is solved using semidefinite programming tools we explore the geometric, algebraic, and computational implications of the presence of discrete symmetries in semidefinite programs. It is shown that symmetry exploitation allows a significant reduction in both matrix size and number of decision variables. This result is applied to semidefinite programs arising from the computation of sum of squares decompositions for multivariate polynomials. The results, reinterpreted from an invariant-theoretic viewpoint, provide a novel representation of a class of nonnegative symmetric polynomials. The main theorem states that an invariant sum of squares polynomial is a sum of inner products of pairs of matrices, whose entries are invariant polynomials. In these pairs, one of the matrices is computed based on the real irreducible representations of the group, and the other is a sum of squares matrix. The reduction techniques enable the numerical solution of large-scale instances, otherwise computationally infeasible to solve.Comment: 38 pages, submitte