10 research outputs found
Bioinformatics
This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here
Recommended from our members
INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY
INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF
AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY
Fatima Magdi Hamza Baldo
This research aims to utilise ligand-based target prediction to (i) understand the mechanism
of action of African natural products (ANPs), (ii) help identify patterns of phylogenetic use in
African traditional medicine and (iii) elucidate the mechanism of action of phenotypically
active small molecules and natural products with anti-trypanosomal activity.
In Chapter 2 the objective was to utilise ligand-based target prediction to understand the
mechanism of action of natural products (NPs) from African medicinal plants used against
cancer. The Random Forest classifier used in this work compares the similarity of the input
compounds from the natural product dataset with compound-target combinations in the
training set. The more similar they are in structure, the more likely they are to modulate the
same target. Natural products from plants used against cancer in Africa were predicted to
modulate targets and pathways directly associated with the disease, thus understanding their
mechanism of action e.g. “flap endonuclease 1” and “Mcl-1”. The “Keap1-Nrf2 Pathway”
and “apoptosis modulation by HSP70”, two pathways previously linked to cancer (which are
not currently targeted by marketed drugs, but have been of increasing interest in recent years)
were predicted to be modulated by ANPs.
In Chapter 3, we aimed to identify phylogenetic patterns in medicinal plant use and the role
this plays in predicting medicinal activity. We combined chemical, predicted target and
phylogenetic information of the natural products to identify patterns of use for plant families
containing plant species used against cancer in African, Malay and Indian (Ayurveda)
traditional medicine. Plant families that are close phylogenetically were found to produce
similar natural products that act on similar targets regardless of their origin. Additionally,
phylogenetic patterns were identified for African traditional plant families with medicinal
species used against cancer, malaria and human African trypanosomiasis (HAT). We
identified plant families that have more medicinal species than would statistically be expected
by chance and rationalised this by linking their activity to their unique phyto-chemistry e.g.
the napthyl-isoquinoline alkaloids, uniquely produced by Acistrocladaceae and
Dioncophyllaceae, are responsible for anti-malarial and anti-trypanosome activity.
In Chapter 4, information from target prediction and experimentally validated targets was
combined with orthologue data to predict targets of phenotypically active small molecules
and natural products screened against Trypanosoma brucei. The predicted targets were
prioritised based on their essentiality for the survival of the T. brucei parasite. We predicted
orthologues of targets that are essential for the survival of the trypanosome e.g. glycogen
synthase kinase 3 (GSK3) and rhodesain. We also identified the biological processes
predicted to be perturbed by the compounds e.g. “glycolysis”, “cell cycle”, “regulation of
symbiosis, encompassing mutualism through parasitism” and “modulation of development of
symbiont involved in interaction with host”.
In conclusion, in silico target prediction can be used to predict protein targets of natural
products to understand their molecular mechanism of action. Phylogenetic information and
phytochemical information of medicinal plants can be integrated to identify plant families
with more medicinal species than would be expected by chance
Investigating the mode of action of AN5568, a novel therapeutic against African trypanosomiasis
No abstract available
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
Recommended from our members
Genome-wide microscopy screening identifies links across processes including a conserved connection between DNA damage control and the microtubule cytoskeleton
Previous PhD students in the lab created a method for large-scale, high-content microscopy screening of a cell library consisting of over 3000 single mutant strains of the fission yeast, Schizosaccharomyces pombe. Each strain has one nonessential gene knocked-out, allowing investigation of the resulting phenotypes. I report the implementation and completion of this screen; developing methods to ensure reliable and accurate results through inclusion of many controls across multiple screening repeats. In total, over 4.5 million images from approximately 19 000 biologically independent cell populations were imaged and analysed.
All strains screened contained GFP-labelled tubulin (GFP-Atb2) allowing visualisation of the microtubule polymer network and its organisation in cells, a feature that is conserved across eukaryotes and simplified in S. pombe, making it easy to study. Examination of cell outlines and microtubule patterns was used to study three cell processes: the shape of cells, the organisational pattern of interphase microtubules and the cell cycle stage of cells, as judged by microtubule pattern. Comparison with extensive data from wild-type cells led to the identification of 262 factors that influence one or more of these cell processes.
I go on to biologically validate some of the outcomes from the screen, leading to a publication in Developmental Cell reporting the screen, its findings and the online genomic resource SYSGRO. I then focus on a group of mutants that suggest a connection between the DNA damage response (DDR) and microtubule organisation. From here I show that the DDR induces elongation of microtubule bundles in response to the DDR kinases, ATM and ATR. I begin to reveal factors that may mediate this response and finally, I provide evidence to suggest that the same mechanism is conserved in cultured human cells (Hc3716-hTERT), which may go some way to explaining clinical results showing a beneficial effect of microtubule destabilisation in conjunction with cancer therapies
2018 GREAT Day Program
SUNY Geneseo’s Twelfth Annual GREAT Day.https://knightscholar.geneseo.edu/program-2007/1012/thumbnail.jp
Ultrasensitive detection of toxocara canis excretory-secretory antigens by a nanobody electrochemical magnetosensor assay.
peer reviewedHuman Toxocariasis (HT) is a zoonotic disease caused by the migration
of the larval stage of the roundworm Toxocara canis in the human host.
Despite of being the most cosmopolitan helminthiasis worldwide, its
diagnosis is elusive. Currently, the detection of specific immunoglobulins
IgG against the Toxocara Excretory-Secretory Antigens (TES), combined
with clinical and epidemiological criteria is the only strategy to diagnose
HT. Cross-reactivity with other parasites and the inability to distinguish
between past and active infections are the main limitations of this
approach. Here, we present a sensitive and specific novel strategy to
detect and quantify TES, aiming to identify active cases of HT. High
specificity is achieved by making use of nanobodies (Nbs), recombinant
single variable domain antibodies obtained from camelids, that due to
their small molecular size (15kDa) can recognize hidden epitopes not
accessible to conventional antibodies. High sensitivity is attained by the
design of an electrochemical magnetosensor with an amperometric readout
with all components of the assay mixed in one single step. Through
this strategy, 10-fold higher sensitivity than a conventional sandwich
ELISA was achieved. The assay reached a limit of detection of 2 and15
pg/ml in PBST20 0.05% or serum, spiked with TES, respectively. These
limits of detection are sufficient to detect clinically relevant toxocaral
infections. Furthermore, our nanobodies showed no cross-reactivity
with antigens from Ascaris lumbricoides or Ascaris suum. This is to our
knowledge, the most sensitive method to detect and quantify TES so far,
and has great potential to significantly improve diagnosis of HT. Moreover,
the characteristics of our electrochemical assay are promising for the
development of point of care diagnostic systems using nanobodies as a
versatile and innovative alternative to antibodies. The next step will be the
validation of the assay in clinical and epidemiological contexts