Chromosomal in situ suppression hybridization of human gonosomes and autosomes and its use in clinical cytogenetics

DNA libraries from sorted human gonosomes were used selectively to stain the X and Y chromosomes in normal and aberrant cultured human cells by chromosomal in situ suppression (CISS-) hybridization. The entire X chromosome was stained in metaphase spreads. Interphase chromosome domains of both the active and inactive X were clearly delineated. CISS-hybridization of the Y chromosome resulted in the specific decoration of the euchromatic part (Ypter-q11), whereas the heterochromatic part (Yq12) remained unlabeled. The stained part of the Y chromosome formed a compact domain in interphase nuclei. This approach was applied to amniotic fluid cells containing a ring chromosome of unknown origin (47,XY; +r). The ring chromosome was not stained by library probes from the gonosomes, thereby suggesting its autosomal origin. The sensitivity of CISS-hybridization was demonstrated by the detection of small translocations and fragments in human lymphocyte metaphase spreads after irradiation with 60Co-gamma-rays. Lymphocyte cultures from two XX-males were investigated by CISS-hybridization with Y-library probes. In both cases, metaphase spreads demonstrated a translocation of Yp-material to the short arm of an X chromosome. The translocated Y-material could also be demonstrated directly in interphase nuclei. CISS-hybridization of autosomes 7 and 13 was used for prenatal diagnosis in a case with a known balanced translocation t(7;13) in the father. The same translocation was observed in amniotic fluid cells from the fetus. Specific staining of the chromosomes involved in such translocations will be particularly important, in the future, in cases that cannot be solved reliably by conventional chromosome banding alone

Quantum extension of European option pricing based on the Ornstein-Uhlenbeck process

In this work we propose a option pricing model based on the Ornstein-Uhlenbeck process. It is a new look at the Black-Scholes formula which is based on the quantum game theory. We show the differences between a classical look which is price changing by a Wiener process and the pricing is supported by a quantum model

Optimization-based Eukaryotic Genetic Circuit Design (EuGeneCiD) and modeling (EuGeneCiM) tools: Computational approach to synthetic biology

Synthetic biology has the potential to revolutionize the biotech industry and our everyday lives and is already making an impact. Developing synthetic biology applications requires several steps including design and modeling efforts which may be performed by in silico tools. In this work, we have developed two such tools, Eukaryotic Genetic Circuit Design (EuGeneCiD) and Modeling (EuGeneCiM), which use optimization concepts and bioparts including promotors, transcripts, and terminators in designing and modeling genetic circuits. EuGeneCiD and EuGeneCiM preclude problematic designs leading to future synthetic biology application development pipelines. EuGeneCiD and EuGeneCiM are applied to developing 30 basic logic gates as genetic circuit conceptualizations which respond to heavy metal ions pairs as input signals for Arabidopsis thaliana. For each conceptualization, hundreds of potential solutions were designed and modeled. Demonstrating its time-dependence and the importance of including enzyme and transcript degradation in modeling, EuGeneCiM is used to model a repressilator circuit

Using EuGeneCiD and EuGeneCiM computational tools for synthetic biology

Synthetic biology often relies on the design of genetic circuits, utilizing ‘‘bio parts’’ (modular DNA pieces) to accomplish desired responses to external stimuli. While such designs are usually intuited, detailed here is a computational approach to synthetic biology design and modeling using optimization-based tools named Eukaryotic Genetic Circuit Design and Modeling. These allow for designing and subsequent screening of genetic circuits to increase the chances of in vivo success and contribute to the development of an application development pipeline. For complete details on the use and execution of this protocol, please refer to Schroeder, Baber, and Saha (2021)

A urinary Common Rejection Module (uCRM) score for non-invasive kidney transplant monitoring.

A Common Rejection Module (CRM) consisting of 11 genes expressed in allograft biopsies was previously reported to serve as a biomarker for acute rejection (AR), correlate with the extent of graft injury, and predict future allograft damage. We investigated the use of this gene panel on the urine cell pellet of kidney transplant patients. Urinary cell sediments collected from patients with biopsy-confirmed acute rejection, borderline AR (bAR), BK virus nephropathy (BKVN), and stable kidney grafts with normal protocol biopsies (STA) were analyzed for expression of these 11 genes using quantitative polymerase chain reaction (qPCR). We assessed these 11 CRM genes for their abundance, autocorrelation, and individual expression levels. Expression of 10/11 genes were elevated in AR when compared to STA. Psmb9 and Cxcl10could classify AR versus STA as accurately as the 11-gene model (sensitivity = 93.6%, specificity = 97.6%). A uCRM score, based on the geometric mean of the expression levels, could distinguish AR from STA with high accuracy (AUC = 0.9886) and correlated specifically with histologic measures of tubulitis and interstitial inflammation rather than tubular atrophy, glomerulosclerosis, intimal proliferation, tubular vacuolization or acute glomerulitis. This urine gene expression-based score may enable the non-invasive and quantitative monitoring of AR

Development of helical, fish-inspired cross-step filter for collecting harmful algae

A new filter was developed to collect harmful algae colonies by adapting the cross-step filtration structures and mechanisms discovered recently in filter-feeding fish. Extending beyond previously published models that closely emulated the basic morphology of the fish, the new cross-step filter\u27s major innovations are helical slots, radial symmetry, and rotation as an active anti-clogging mechanism. These innovations enable the transport of concentrated particles to the downstream end of the filter. This advance was made possible by recognizing that biologically imposed constraints such as bilateral symmetry do not apply to human-made filters. The use of helical slots was developed in a series of iterative tests that used water-tracing dye and algae-sized microspheres. The major products of the iterative tests were refinements in the helical design and an understanding of how varying the major structural parameters qualitatively influenced fluid flow and filter performance. Following the iterative tests, the clogging behavior of select filters was quantified at high particle concentrations. Vortices in the helical filter were effective at reducing clogging in the center of the slots. By considering the design space that is free of the biological constraints on the system and exploring the effects of variations in major structural parameters, our work has identified promising new directions for cross-step filtration and provided key insights into the biological system

Evaluation of the Effect of Vaccination Side on Subsequent Halter Breaking Side Preference in Cattle

The quality of animal-human interactions is important, as negative interactions may result in an animal being difficult to handle. Halter breaking is used as a means to make the process of moving and securing a calf easier, and theoretically should minimize stress for both the animal and handler. There are numerous ways that people can halter break a calf, for example tying up the cattle in barns for a defined period of time, touching the cattle for the first time using combs or using a “Talk and Touch” method. Anecdotal evidence shows with halter breaking that cattle have a side preference and it has been hypothesized that this side preference may be related to the side that vaccinations were given. Therefore, the goal of this study was to determine if a calf indicates a side approachability preference during halter breaking that is dependent on vaccination side. A total of 20 crossbred Angus/Simmental steers from Iowa State University’s (ISU) breeding herd were used. Steers were between 7 and 9 mo of age, averaging 272 kg BW. Steer was the experimental unit. A 2 (left or right neck side for vaccination) x 2 (left or right approach side) factorial arrangement of treatments was compared. One month after weaning, each steer had a nylon halter affixed to his head 2 d prior to the steer side preference test. Each handler was blind to vaccination side. Approach side for each steer had been randomly assigned prior to the beginning of the trial. Halter breaking methodology was conducted over five defined steps. Students were asked at the end of the 1-h period to conclude if the calf had a left, right, or no side preference. Data was analyzed using PROC GLIMMIX for the effects of vaccination side on subsequent halter breaking side preference. There was no difference observed between halter breaking side preference in relation to vaccination side (P \u3e 0.05). In conclusion, with this data set there was no halter breaking preference side related to vaccines given, indicating that the calves did not negatively associate humans with restraint and injections. This is helpful in understanding animal/human interactions as well as ability to approach an animal after vaccinations. This also implies that strategies such as the “Talk and Touch” method are useful in keeping calves calm and comfortable during halter breakin