Yossy Machluf

Integrating bioinformatics into senior high school: design principles and implications

Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Visualization of mRNA expression in the zebrafish embryo.

Examination of spatial and temporal gene expression pattern is a key step towards understanding gene function. Therefore, in situ hybridization of mRNA is one of the most powerful and widely used -techniques in biology. Recent advances allow the reliable and simultaneous detection of mRNA transcripts, or combinations of mRNA and protein, in zebrafish embryos.Here we describe a standard protocol for visualizing the precise expression pattern of a single transcript or multiple gene products. The procedure employs fixation and permeabilization of embryos, followed by hybridization with tagged antisense riboprobes. Excess probes are then washed and hybrids are detected by enzyme-mediated immunohistochemistry utilizing either chromogenic or fluorescent substrates.

Adolescent BMI at Northern Israel: From Trends, to Associated Variables and Comorbidities, and to Medical Signatures.

AbstractThe increasing prevalence of abnormal body mass index (BMI), mainly obesity, is becoming a significant public health problem. This cross-sectional study aimed to provide a comprehensive view of secular trends of BMI, and the associated socio-demographic variables and comorbidities among adolescents with abnormal BMI. Individuals of the study population were born mainly between 1970 and 1993, and were examined at 16 to 19 years of age during the years 1987 to 2010, at 1 conscription center in the northern district of Israel.The study population included 113,694 adolescents. Univariate and multivariable logistic regression models were used to investigate the associations between BMI categories, socio-demographic variables, and medical conditions.A downward trend in the prevalence of normal BMI among both male and female adolescents was obtained, while trends of overweight and obesity (in both genders) and underweight (only among females) rose. Socio-demographic variables such as religion, education, family-related parameters, residential environment, country of birth, and origin were all associated with different risks for abnormal BMI. Obesity was associated with higher risk for hyperlipidemia, endocrine disorders (only in males), knee disorders, and hypertension type I + II (in both genders). Overweight was associated with knee disorders (only in females). Underweight, exclusively in males, was associated with increased risk for endocrine disorders, proteinuria, and cardiac disorders. Hierarchical clustering analysis revealed the intricate relations between gender, BMI, and medical signatures. It brought to light novel clusters of diseases that were abundant among populations having above-normal BMI or underweight males. Furthermore, above-normal BMI was associated with a lower rate of cardiac anomalies and scoliosis/kyphosis, whereas being underweight was associated with a lower risk for hypertension and flat foot.This study provides a reliable and in-depth view of secular trends in height, weight, and BMI of male and female adolescents. It supports previous associations between abnormal BMI and demographic variables and comorbidities, while uncovering novel associations, mainly regarding medical signatures of each gender–BMI group. This might lead to better monitoring, early detection, prevention, and treatment of various conditions associated to abnormal BMI categories and gender groups.

Coordinated computerized systems aimed at management, control, and quality assurance of medical processes and informatics.

PURPOSE As part of the routine work of the medical committees in the Israel Defense Forces, a unique nationwide computerized control system is being implemented to assess and manage medical processes. The purpose of this paper is to report on that implementation. DESIGN/METHODOLOGY/APPROACH The computerized system consists of three main components: a specific status indicating the processes in each file, an appointment system, and an internal computerized system that uses a magnetic card for the regulation of the local waiting lists. FINDINGS The combined computerized system improves the control and management of the medical processes and informatics from the point-of-view of both the patients and system operators. Different parameters of quality control regarding the medical and administrative processes are assessed (such as efficiency), and solutions are sought. Computerized system-based design and re-allocation of human and medical resources were implemented according to the capacities and limitations of the medical system. A reduction in the daily number of invited recruits improved the quality of the medical encounters. Specific combined status codes were introduced for the efficient planning of the medical encounters. Implementation and automation of medical regulations and procedures within the computerized system make the latter play a key role and serve as a control tool during the decision-making process. ORIGINALITY/VALUE The computerized system allows efficient follow-up and management of medical processes and informatics, led to a better utilization of human and medical resources, and becomes a component of the decision making by the system operators and the administrative staff. Such a system could be used with success in clinics, hospitals, and other medical facilities.

From a Quality Assurance and Control System for Medical Processes, Through Epidemiological Trends of Medical Conditions, to a Nationwide Health Project

Yossy Machluf1,2, Amir Navon1, Avi Yona1, Avinoam Pirogovsky1,3, Elio Palma1,4, Orna Tal5, Nachman Ash6, Avi Cohen1 and Yoram Chaiter1 1Quality Assurance and Control Committee, Medical Corps, IDF, 2Weizmann Institute of Science, Rehovot, 3Head of Standards and Regulation Department in the Division of Community Medicine, Ministry of Health, Tel Aviv, 4Head of Department of Occupational Medicine, Clalit Health Services, Afula, 5Israeli Center for Technology Assessment in Health Care; The Gertner Institute for Epidemiology and Health Policy Research, Head of Emerging Technologies Unit, Tel Aviv, 6Chief Medical Officer, Medical Corps, IDF, Israel

Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency.

BackgroundIn recent years, the perception of transposable genetic elements has changed from “junk DNA” to a focus of interest when appearing near or inside genes. Bov-A2 is a short interspersed nuclear element (SINE) that was first found in Bovidae and later in other ruminants. This retroposon is mostly used as a marker for phylogenetic analysis.ResultsWe describe insertions of Bov-A2 in the promoter region of TP53, a key tumor suppressor gene that is indispensable for diverse developmental processes, in Antilopinae and Tragelaphini (belonging to the Bovinae subfamily). In Tragelaphini two Bov-A2 elements were inserted sequentially, whereas in 5 tribes of Antilopinae only one Bov-A2 element was inserted, in a different site and reverse orientation. The entrance site in both cases employed short palindromes that can form hairpin secondary structures. Interestingly, mutations that create or disrupt base pairing in the palindrome sequence dictated the presence or absence of Bov-A2, such as in the domestic cow and buffalo, which lack Bov-A2. Transcription factor binding site analysis revealed unique binding sites for STAT3 and NFκB within the Bov-A2 sequence, which together with TP53 itself are known to play a crucial role in mammary involution.ConclusionsThis report demonstrates how short palindromes serve as hot spots for Bov-A2 retroposon insertion into the mammalian genome. The strict correlation between point mutation in the palindromes and the presence/absence of Bov-A2 retroposon insertions, questions the use of singular insertion events as valid phylogenetic markers inside families. Bov-A2 insertion into the TP53 promoter in Antilopinae and Tragelaphini may not only provide a genetic network that regulates mammary involution, but can also answer the need for rapid mammary involution in Savanna antelopes after weaning, partially in response to predation stress. The absence of Bov-A2 in domestic bovids may constitute the molecular background for greater lactation persistency.

Mammal domestication and the symbiotic spectrum

In their paper in PNAS, Weissbrod et al. (1) conclude that mice adapted to the temporary sedentary lifestyle of humans during the Late Pleistocene and underwent a domestication process driven by a competitive advantage for commensal mice in the evolving, long-term human settlements. The authors expand the possibility of an early interaction between wild mammals and humans to other wild species, wild boars and wolves, as examples of “following commensal pathways before developing long-term mutualism characteristic of domestication” (1). We wish to deliberate on both the process and its nature, with … [↵][1]1To whom correspondence should be addressed. Email: yarond{at}gri.org.il. [1]: #xref-corresp-1-1

Cardiac anomalies and associated comorbidities in a large adolescent population

Abstract Objective: To determine the prevalence, secular trends and associations of heart disease in a large unscreened, otherwise basically healthy, adolescent population. Subjects and methods: Cross-sectional study of the cardiac status of 113,694 adolescents from the northern district of Israel, who completed the profiling process between the ages of 16 and 19, including all essential measures over a 22-year period. Results of imaging were categorized as either isolated valvar or structural abnormalities, and their clinically significant subgroups defined prospectively. The findings were correlated with the socio-demographic and anthropometric data and non-cardiac health conditions. Results: Of those sent for echocardiography, 1257 (0.93% of the total population) had isolated valvar disease and 216 (0.19%) had structural abnormalities, with 20% of both groups considered significant. Females had lower prevalence of heart disease. There was peak prevalence in the second 5-year period. Tall subjects or a past history of rheumatic fever had more valvar abnormalities. Thin subjects or those with skeletal anomalies had more structural abnormalities. Significant valvar and structural anomalies were more common in subjects with learning disorders, endocrine disorders and diabetes mellitus. Fewer valvar abnormalities were diagnosed in obese subjects. Heart disease was more common in those with non-solid tumors. Conclusion: Appreciable numbers of potentially healthy adolescents were found to have heart disease. There appeared to be an association with body size, skeletal abnormalities and relatively common medical disorders, the cause of which remains to be determined in prospective studies that could change the way common adolescent disease should be followed.

Formation of multimeric antibodies for self-delivery of active monomers

Abstract Proteins and peptides have been used as drugs for almost a century. Technological advances in the past 30 years have enabled the production of pure, stable proteins in vast amounts. In contrast, administration of proteins based on their native active conformation (and thus necessitating the use of subcutaneous injections) has remained solely unchanged. The therapeutic anti-HER2 humanized monoclonal immunoglobulin (IgG) Trastuzumab (Herceptin) is a first line of the treatment for breast cancer. Chicken IgY is a commercially important polyclonal antibody (Ab). These Abs were examined for their ability to self-assemble and form ordered aggregates, by several biophysical methods. Atomic force microscopy analyses revealed the formation of multimeric nanostructures. The biological activity of multimeric IgG or IgY particles was retained and restored, in a dilution/time-dependent manner. IgG activity was confirmed by a binding assay using HER2 + human breast cancer cell line, SKBR3, while IgY activity was confirmed by ELISA assay using the VP2 antigen. Competition assay with native Herceptin antibodies demonstrated that the binding availability of the multimer formulation remained unaffected. Under long incubation periods, IgG multimers retained five times more activity than native IgG. In conclusion, the multimeric antibody formulations can serve as a storage depositories and sustained-release particles. These two important characteristics make this formulation promising for future novel administration protocols and altogether bring to light a different conceptual approach for the future use of therapeutic proteins as self-delivery entities rather than conjugated/encapsulated to other bio-compounds.

The significance of human spermatozoa vacuoles can be elucidated by a novel procedure of array comparative genomic hybridization

STUDY QUESTION Is there an association between spermatozoon genomic stability and vacuolar morphology and location? SUMMARY ANSWER The genomic stability of spermatozoa is associated with specific characteristics of vacuolar morphology (depth) and location (cellular compartment, i.e. nucleus and equatorial region). WHAT IS KNOWN ALREADY Genetic anomalies in sperm are correlated with semen abnormalities, yet the advantage of morphologically based selection of spermatozoa for IVF according to current criteria is controversial. Selection criteria based on the number of vacuoles and their size have been proposed and are widely applied. Nevertheless, it has not improved the ICSI success rates, suggesting the currently used vacuole criteria are incomplete. STUDY DESIGN, SIZE, DURATION Normal sperm according to Motile Sperm Organelle Morphology Examination criteria (MSOME) and common vacuole grading were evaluated. An additional evaluation of sperm vacuole morphology according to novel vacuole criteria (i.e. location and depth) was conducted. An assessment to align these specific vacuolar morphology features with genomic stability was conducted among spermatozoa from infertile patients and healthy fertile donors aged 24-38 between June 2015 and July 2016. PARTICIPANTS/MATERIALS, SETTING, METHODS Single spermatozoa (n = 53) from 16 infertile patients and 14 fertile donors were morphologically and genetically evaluated. Each spermatozoon was examined morphologically, by ultra-magnification ×6300, and genetically by a novel comparative genomic hybridization protocol, without the use of reference DNA, to assess chromosomal instability as evident by copy number variations (CNV). MAIN RESULTS AND THE ROLE OF CHANCE We established an association between genomic stability and vacuolar morphology as a base for a new classification according to novel vacuolar criteria, specifically depth and location. Genomic instability was found to be related to these two main features of vacuoles and, surprisingly not to the number and size of vacuoles as in the previously proposed classifications. High CNV spermatozoa were characterized by vacuoles located in the nucleus and/or equatorial segment or by deep vacuoles, while, low CNV spermatozoa were characterized by a complete lack of vacuoles or non-deep vacuoles not located in the nucleus/equatorial segment. A putative threshold of ~265 CNV was deduced to distinguish between genetically stable and unstable spermatozoa, and 94% of the tested spermatozoa segregated accordingly. LIMITATIONS REASONS FOR CAUTION A relatively small sample of spermatozoa were examined-53 in total. However, the association between vacuoles location and morphology and genomic stability was significant. This is the first study evaluating spermatozoon genomic stability with respect to vacuole morphology according to novel vacuole criteria (i.e. location and depth) and further investigation is warranted to verify the value of these criteria in larger sample size clinical studies. WIDER IMPLICATIONS OF THE FINDINGS Our results, which are based on spermatozoon vacuoles morphological classification and genomic parameters, indicate an association between vacuoles morphology and location and genomic stability. The data presented herein suggest the existence of subpopulations of spermatozoa potentially appropriate for IVF-ICSI, as they appear normal according to the current MSOME and vacuoles classification, however they are almost certainly genetically damaged. As current criteria have yet to achieve an unequivocal evaluation of the implantation potential of a given spermatozoon, we propose novel criteria, based on specific vacuolar morphological traits; depth and location, as these were found aligned with genomic findings. STUDY FUNDING/COMPETING INTEREST(S) No funding was received for this study. The authors have no conflict of interest to declare. TRIAL REGISTRATION NUMBER N/A.