Miracle-dz/UniFAR-FTUs huggingface dataset:
Editing T cell specificity

Allogeneic hematopoietic stem cell transplantation is considered to be the main means of treatment for hematological malignancies. However, disease relapse and graft versus host disease remain the major cause of death post transplantation. To reduce the risk of graft versus host disease and in order to improve the graft versus leukemia effect, genetically engineered T-cells are used to express tumor specific antigens. This is either through the transfer of a recombinant antigen-specific T cell receptor (TCR) or through the introduction of antibody-like recognition in chimeric antigen receptors (CARs) toward tumor-associated antigens. These methods have made substantial advances. Nevertheless, the complexity in modifying and producing autologous specific T-cell products for each patient is a major barrier to the broader application of this approach. In this context, the ability to generate an “off-the-shelf” mismatched donor-derived therapeutic T cell product was investigated. To overcome HLA barriers and to eliminate the risk of graft versus host disease, tailored transcription activator-like effector nucleases (TALENs) knocking out the expression of endogenous T cell receptor was utilised. Also, the potential of engineered meganucleases and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) to disrupt the genomic sequence of the T cell receptor was evaluated. Large numbers of recent clinical trials have suggested that in vivo persistence and expansion having a potent anti-tumor activity of the genetically engineered T cells is crucial to have a robust clinical response. In order to generate a T cell product possessing these previous features, we have investigated the ability to engineer naive cord blood T cells toward specific tumor antigens. Due to their naivety, the higher telomeres activity, low graft-versus-hostdisease, amongst several other features, have the potential of making cord blood an optimal source for the production of a universal allogeneic engineered T cell therapy. Moreover, preclinical models have demonstrated that culturing naive T cells in the presence of interleukin-7 and interleukin-15 might retain the modified cells in their naive like phenotype. In conclusion, delivery of CD19CAR genes using lentiviral vectors into naive cord blood T cells could form the basis of generating a universal cell bank of therapeutic T cells against B cell lymphoma. With further optimisation to improve efficiency, this could be combined with TALENs for site-specific disruption of the endogenous T cell receptor to eradicate the risk of graft-versus-host disease
A Simulation Analysis and Screening of Deleterious Non-Synonymous Single Nucleotide Polymorphisms (SNPs) in Human CDKN1A Gene

CDKN1A also known as p21cip1/p21WAF1, is a cyclin dependent kinase 1, interacts with proliferating cell nuclear antigen (PCNA) resulting in cell cycle inhibition in human. Polymorphism in the CDKN1A gene is related to the onset of several cancers and Alzheimer’s disease. Non-synonymous single nucleotide polymorphisms (nsSNPs), which reside in the coding region of a gene, might cause loss of function in the corresponding protein. In silico analysis used in this study exerts many different algorithms such as SIFT, Polyphen-2, Predict SNP, I-Mutant 3.0 and Mupro etc. to screen out the most deleterious nsSNPs and their effect on the corresponding protein. Following the screening of 118 nsSNPs, finally, 12 missense SNPs (R19C (C→T), G23D (A→G), V25G (G→T), V25L (C→G), Q29P (A→C→G), F51L (C→T), E56K (A→G), T57I (C→T), G61R (C→G), G61D (A→G), Y151C (A→G) and R156W (C→G→T) were predicted to have deleterious effect by all the algorithms. Of them, R19C, G23D, F51L, Y151C and R156W occurred at the highly conserved site. G23D, F51L variants also occurred at the CDI domain. Homology structure built by MUSTER, Phyre-2, RaptorX and Swiss model predicted decrease of energy in mutant models. GV-GD scores predicted only two variants as neutral (V25L, F51L). Molecular features behind the deleterious effect of these nsSNPs was evaluated in this study.
Landscape‐scale habitat assessment for an imperiled avian species

A comprehensive understanding of wildlife habitat suitability requires landscape‐scale assessments that provide the framework for subsequent integration with local‐scale relationships. To elucidate the functional role of habitat characteristics at large scales it is necessary to understand how abundance is related to important landscape characteristics. We estimated male greater sage‐grouse Centrocercus urophasianus abundance on leks relative to sagebrush availability, landscape connectivity and anthropogenic infrastructure densities within landscapes surrounding leks from 2006 to 2013 using binomial N‐mixture models. We focused on Wyoming, as the state will play a critical role in the long‐term persistence of greater sage‐grouse due to its relatively robust populations, widespread sagebrush habitats and innovative, large‐scale conservation approaches. Landscapes associated with higher abundance of males on leks were characterized as highly connected, sagebrush‐dominated areas with limited energy development. These modeled relationships were used to evaluate spatial and temporal changes in the landscape‐scale integrity of areas supporting the majority of the greater sage‐grouse populations in Wyoming (i.e. core areas). By assessing relative changes in abundance over time, our models indicated that most of the habitat within core areas (86%) exhibited landscape conditions conducive to supporting medium or large greater sage‐grouse populations that were stable or increasing through time. Larger populations were associated with larger, more centrally located core areas. Conversely, core areas supporting relatively small or declining populations were located along range margins in the eastern portion of the state. The landscape‐scale habitat relationships we developed can be used in combination with local‐scale assessments to generate a more complete picture of greater sage‐grouse habitat suitability.
Consistent temporal variation in the diet of an endangered alpine lizard across two south-eastern Australian sky-islands

A species ’ diet and feeding strategy directly affect ﬁ tness and environmental interactions. Understanding spatial and temporal variation in diets can identify key resources, inform trophic relationships, and assist in managing threatened species. The nationally endangered Guthega skink, Liopholis guthega , is restricted to two isolated Australian alpine plateaux, the Bogong High Plains (BHP) in Victoria and Kosciuszko National Park (KNP) in New South Wales. We compared this species ’ foraging ecology over the summer period between these ‘ sky-islands ’ separated by ~ 100 km of lowland valleys. Scat composition did not differ between the two lizard populations, despite differences in the invertebrate assemblages present. However, L. guthega diet varied temporally over summer at both locations. Invertebrates, predominantly Hymenoptera and Coleoptera, were the dominant food group in early summer (78% volume (V), 100% frequency occurrence (F)) and mid-summer (80% V, 100% F). A signi ﬁ cant dietary shift occurred in late summer, when lizards consumed predominantly plant material (63% V, 95.5% F), consisting primarily of seasonally abundant berries from the snow beard heath, Acrotham-nus montanus . In contrast to similar-sized Egerniinae species, it appears L. guthega is capable of opportunistically shifting its diet towards plant material in response to temporal variation in resource availability. Furthermore, the prevalence of intact seeds in scats indicates L. guthega may play a signi ﬁ cant role in seed dispersal. Understanding these trophic interactions will assist conservation management of L. guthega , allowing conditions for an already established captive colony to mimic the temporally variable diets present in situ , as well as informing revegetation initiatives aimed at maintaining and expanding wild populations.
Détection de l'activité des éléments transposables chez les plantes cultivées : étude du mobilome par la caractérisation du compartiment extrachromosomique

Les elements transposables (ET) sont des elements genetiques ubiquitaires et potentiellement mobiles dans les genomes eucaryotes. Les genomes hotes ont developpe des mecanismes epigenetiques pour controler et prevenir la proliferation des ET. Neanmoins, certains ET semblent capables de s’activer en reponses a des stress ou a des facteurs developpementaux. Les methodes disponibles pour detecter l’activite transpositionnelle d’un ET sont souvent limitees au stade transcriptionnel ou sont adaptees a des genomes de petite taille. Relativement peu d’ET sont actuellement connus pour etre actifs et les mecanismes specifiques qui les controlent ne sont pas clairement identifies.Durant mes travaux de these, nous avons developpe une strategie de sequencage a haut debit qui permet la detection d’ADN extrachromosomique circulaire (ADNecc) temoignant notamment de l’activite des ET et de la stabilite d’un genome. Ainsi nous avons pu caracteriser chez plusieurs especes le mobilome, defini comme l’ensemble des ADNecc presents dans un tissu.La technique du mobilome-seq s’est averee etre un outil puissant pour la detection des ET actifs notamment chez le riz asiatique Oryza sativa. Notre analyse du mobilome a permis l’identification d’un retrotransposon PopRice actif dans l’albumen (tissu nourricier du grain) chez differentes varietes de riz. Pour la premiere fois chez les plantes, nous avons egalement detecte des insertions somatiques d’ET par re-sequencage de genome entier. A partir de nos resultats, nous avons combine nos donnees mobilomiques avec une analyse GWAS pour proposer des pistes afin d’identifier de nouveaux mecanismes de regulation de cet element.En parallele, nous avons applique la technique du mobilome-seq a differents organismes animaux et vegetaux revelant ainsi des specificites de mobilome propre a chaque espece. Nos travaux en collaboration avec d’autres equipes ont notamment contribue a preciser le role de l’ARN polymerase II dans le controle des ET chez O. sativa et a mettre en evidence le lien entre la presence d’ADNecc viral et la reponse immunitaire chez Drosophila melanogaster.Mes travaux de these ouvrent des perspectives pour l’etude du mobilome, ce repertoire genomique encore largement inexplore et qui se revele etre a la fois une source d’information au niveau des mouvements des ET mais aussi de la stabilite des genomes. L’etude future des mobilomes promet d’apporter des reponses sur notre comprehension de la dynamique des genomes.
Critical period for murine olfactory map formation

Formation of neural circuits in the brain is sensitive to deprivation of neural activity during the critical period. In the last few decades, the critical period has been studied extensively. These studies are primarily focused on the development of receptive fields in the cortex. Mechanisms regulating the connection between sensory neurons and their central targets during the critical period remain unknown. In this study, together with other members of the Yu lab, I performed a series of experiments in mice to perturb the projection pattern of olfactory sensory neurons (OSNs) during postnatal development. I observed a critical period during the formation of the olfactory circuit. Neurons generated during and after the critical period adopted different mechanisms in axon targeting. The early-born neurons were able to form converging projection into single glomerulus de novo. They also possessed the ability to correct mis-targeted axons. The late born neurons relied on existing axon tracks to target the correct glomeruli. Through genetic chronicle tracing experiments, I was able to demonstrate that early born neurons had a shorter life span, a faster turnover rate, and an increased axon projection plasticity compared to the late born neurons. Because of these unique characteristics, I defined the early born OSNs as “settler neurons”. Genetic ablation of settler neurons resulted in a disrupted axon projection pattern. Transgenic expression of Bcl2, an anti-apoptotic gene, in the OSNs extended the life span of the settler neurons beyond the critical period. The existence of the settler neurons after the critical period promoted the axon exuberant growth. It also affected the OSNs’ axon projection pattern. Transcriptome analysis revealed a genetic switch during the critical period. Different sets of transcription regulators, axon guidance molecules, and signaling molecules were expressed between the settler neurons and the OSNs born afterwards. I identified a G protein coupled receptor, Frizzled 1 (Fzd1), as a critical regulator of the critical period in the olfactory system. Ectopic expression of Fzd1 after the closure of the critical period enabled OSN axons to grow exuberantly and caused mis-targeting phenotype. Removing Frizzled 1 postponed the closure of the critical period. Finally, I showed that Fzd1 was physically associated with olfactory receptors (ORs). This interaction provided a molecular basis for Fzd1 to influence OSN’s axon guidance.
Cellular Mechanisms of Ionoregulation in the Gill of Japanese Medaka and Rainbow Trout

Euryhaline fishes are capable of adapting to a wide range of salinities such as freshwater, brackish water or seawater. Through the combined effort of the gill, kidney and intestine, they are able to osmoregulate to maintain a constant internal hydromineral balance. As the gill is in direct contact with the external environment, it is continuously working to maintain ion and acid/base balance, gas exchange and eliminate nitrogenous waste. Fish in freshwater are subjected to osmotic water gain and diffusional ion loss across the gill and experience the opposite in seawater. Therefore, the gill exhibits extreme plasticity when experiencing a change in external salinity. Osmoregulation in fishes is controlled mainly by the endocrine system. Prolactin is a freshwater-adapting hormone as it decreases epithelial permeability and increases ion-retention in osmoregulatory tissues. This dissertation examines the osmoregulatory function of the gill in two euryhaline teleosts, the Japanese medaka (Oryzias latipes) and rainbow trout (Oncorhychus mykiss). Gill of medaka exposed to seawater and freshwater were used to observe the effect of salinity on the expression of key ion transporters. Hormone in vitro studies were performed to understand the mechanism of prolactin-induced expression of the Na + , Cl cotransporter in medaka gill. Finally, rainbow trout were subjected to ion poor water to expand our understanding of ion retention and ionocyte re-uptake function in a salmonid species. Furthermore, several human diseases are related to (dys)function of osmoregulatory proteins including cancers, inflammatory bowel disease and chronic kidney disease. Because of the adaptability of the gill epithelia, euryhaline teleosts represent a unique model that may help us understand pathologies in human diseases related to epithelial dysfunction. The endocrine system of teleosts is also analogous to the human endocrine system and is therefore valuable to better understand hormone-linked diseases in human such as breast cancer, diabetes and atherosclerosis. The experiments performed in this dissertation demonstrate the ability of euryhaline teleosts to provide an alternative model to study human diseases.
Using citizen science data in integrated population models to inform conservation decision-making

Analysis of animal population status and change are core elements of ecological research and critical for prioritizing conservation actions. Traditionally, count-based data from structured surveys have been the main source of information used to estimate trends and changes in populations. In the past decade, advances in integrated population models (IPMs) have allowed these data to be combined with other data sources (e.g., observations of marked individuals). IPMs have allowed researchers to determine the direction and magnitude of a species’ population trajectory and to test underlying mechanisms. For many species, life-history characteristics (e.g., low site-fidelity), low abundance and/or low detection probability make it difficult to collect sufficient data; thus, IPMs for these species are difficult to employ. We used count data from eBird to estimate population trends for one such species, the tricolored blackbird (Agelaius tricolor). We combined estimates of relative abundance with banding and nesting data. Our joint estimation of demographic rates allowed us to evaluate their individual contributions to the population growth rate. We suggest that investments in increasing reproductive success and recruitment are the most likely conservation strategies to increase the population. The extensive survey efforts of citizen scientists aided the employment of IPMs to inform conservation efforts. Data Accessibility Should the manuscript be accepted, the data supporting the results will be published along with the manuscript. The eBird data used for analyses in this manuscript may be downloaded from https://ebird.org/data/download.
Cytosolic delivery of large supramolecular protein complexes arranged on DNA nanopegboards

A generic methodology for cytosolic delivery of large supramolecular multiprotein complexes into living cells is described that takes advantage of the highly-controllable bottom-up fabrication of protein-decorated DNA nanostructures and the microfluidic “cell squeezing” technique. Therein, cells are deformed upon passage through a narrow constriction leading to formation of transient holes in the cell membrane that enable the diffusion of the protein-DNA nanostructures from the surrounding buffer into the cytosol. A diverse set of multiprotein complexes was assembled on DNA origami nanostructures using streptavidin and the sensitive glucose sensor protein FLIP as model systems. We demonstrate that our approach allows for the direct cytosolic delivery of these multifunctional protein complexes into the cytosol of HeLa cells. We also demonstrate that targeting groups can be incorporated into the protein-DNA nanoassemblies to enable their intracellular targeting to cytosolic compartments, such as the cytoskeleton or nucleus. We believe that this methodology will open up novel strategies for research in fundamental cell biology, such as the reverseengineering of the supramolecular machinery involved in gene regulation, cell signalling, or cell division. Furthermore, direct applications in immunotherapy can be foreseen.
Vulnerability of a specialized pollination mechanism to climate change revealed by a 356-year analysis

Pollination of Ophrys sphegodes by sexual deception of male Andrena nigroaenea bees depends both on male bees emerging before female bees and before flowering, and on the orchid flowering before female bee emergence, so that competition for the services of naive male bees is avoided. Using previously-established relationships between the timing of these phenological events and spring temperature, we model flowering and bee emergence dates from 1659-2014, using Central England Temperature records. All phenological events were predicted to advance significantly over this period, accompanying a trend towards warmer springs. The interval between male and female flight decreased over time, whereas that between male flight and flowering increased. In addition, female flight preceded orchid flowering after warm springs, and it preceded both flowering and male bee flight following the warmest springs. Such reversals in phenology have increased in frequency over the last 356 years. In most years, the Ophrys/Andrena pollination system achieves very limited pollination success. The results presented here suggest that climate warming has changed the timing of the phenological events that are critical to reproductive success in O. sphegodes, and that continuing warming will increase the frequency of years in which this rare orchid suffers complete reproductive failure.
Studies on Heterosis in Pumpkin (Cucurbita moschata Duch. ex. Poir)

Pumpkin (Cucurbita moschata Duch. ex. Poir) is one of the important cucurbitaceous vegetable. It is cultivated throughout the tropical regions of India. It has high productivity, nutritive values, good storability and better transport quality. The immature and mature fruits used as vegetable. In India, pumpkin cultivated in an area of 11,060 hectares with the total production of 2.77 lakh tonnes which have productivity of 25.10 tonnes per hectare during 2014. In Tamil Nadu state, pumpkin grown an area of 1,530 hectares with an annual production of about 37,340 tonnes and productivity of 24.41 tonnes per hectare during 2014 (Saxena and Chander, 2015). Little attention has been given on crop improvement, as compared to International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 03 (2018) Journal homepage: http://www.ijcmas. com
Venturia species form sooty mold-like colonies on leaves of Salix: introducing Venturia fuliginosa sp. nov.

Collection of ascomycetes in the Lesser Khingan Mountains of China led to the discovery of two species of Venturia on Salix, one of which is described and illustrated as a new species-V. fuliginosa in this paper. Venturia fuliginosa forms a sooty mold-like phenotype on the leaf surface of the host, and differs from known species of Venturia in having fusiform, subcylindrical, sometimes obpyriform and mostly aseptate conidia. Phylogenetic inference based on analysis of combined LSU and ITS sequence data, indicate that the new species is closely related to a strain named V. chlorospora (CBS 470.61) isolated from Salix daphnoides in 1958 in France. The second species, Venturia catenospora, is reported for the first time in China.
Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences

Enhancer sequences regulate the expression of genes from afar by providing a binding platform for transcription factors, often in a tissue-specific or context-specific manner. Despite their importance in health and disease, our understanding of these DNA sequences, and their regulatory grammar, is limited. This impairs our ability to identify new enhancers along the genome, or to understand the effect of enhancer mutations and their role in genetic diseases. We trained deep Convolutional Neural Networks (CNN) to identify enhancer sequences in multiple species. We used multiple biological datasets, including simulated sequences, in vivo binding data of single transcription factors and genome-wide chromatin maps of active enhancers in 17 mammalian species. Our deep networks obtained high classification accuracy by combining two training strategies: First, training on enhancers vs. non-enhancer background sequences, we identified short (1-4bp) low-complexity motifs. Second, by replacing the negative training set by adversarial k-order random shuffles of enhancer sequences (thus maintaining base composition while shuttering longer motifs, including transcription factor binding sites), we identified a set of biologically meaningful motifs, unique to enhancers. In addition, classification performance improved when combining positive data from all species together, showing a shared mammalian regulatory architecture. Our results demonstrate that design of adversarial training data, and transfer of learned parameters between networks trained on different species/datasets improve the overall performance and capture biologically meaningful information in the parameters of the learned network. Contact: or.zuk@mail.huji. ac.il, tommy@cs.huji. ac.il