Abstract: Analysis of the human microbiome using metagenomic
sequencing data has demonstrated high ability in discriminating
various human diseases. Raw metagenomic sequencing data require
multiple complex and computationally heavy bioinformatics steps
prior to data analysis. Such data contain millions of short sequences
read from the fragmented DNA sequences and stored as fastq files.
Conventional processing pipelines consist in multiple steps including
quality control, filtering, alignment of sequences against genomic
catalogs (genes, species, taxonomic levels, functional pathways,
etc.). These pipelines are complex to use, time consuming and
rely on a large number of parameters that often provide variability
and impact the estimation of the microbiome elements. Training
Deep Neural Networks directly from raw sequencing data is a
promising approach to bypass some of the challenges associated with
mainstream bioinformatics pipelines. Most of these methods use the
concept of word and sentence embeddings that create a meaningful
and numerical representation of DNA sequences, while extracting
features and reducing the dimensionality of the data. In this paper
we present an end-to-end approach that classifies patients into disease
groups directly from raw metagenomic reads: metagenome2vec. This
approach is composed of four steps (i) generating a vocabulary of
k-mers and learning their numerical embeddings; (ii) learning DNA
sequence (read) embeddings; (iii) identifying the genome from which
the sequence is most likely to come and (iv) training a multiple
instance learning classifier which predicts the phenotype based on
the vector representation of the raw data. An attention mechanism
is applied in the network so that the model can be interpreted,
assigning a weight to the influence of the prediction for each genome.
Using two public real-life data-sets as well a simulated one, we
demonstrated that this original approach reaches high performance,
comparable with the state-of-the-art methods applied directly on
processed data though mainstream bioinformatics workflows. These
results are encouraging for this proof of concept work. We believe
that with further dedication, the DNN models have the potential to
surpass mainstream bioinformatics workflows in disease classification
tasks.
Abstract: A hydrogel from cellulose acetate cross linked with ethylenediaminetetraacetic dianhydride (HAC-EDTA) was synthesized by our research group, and submitted to characterization and biological tests. Cytocompatibility analysis was performed by confocal microscopy using human adipocyte derived stem cells (ASCs). The FTIR analysis showed characteristic bands of cellulose acetate and hydroxyl groups and the tensile tests evidence that HAC-EDTA present a Young’s modulus of 643.7 MPa. The confocal analysis revealed that there was cell growth at the surface of HAC-EDTA. After one day of culture the cells presented spherical morphology, which may be caused by stress of the sequestration of Ca2+ and Mg2+ ions at the cell medium by HAC-EDTA, as demonstrated by ICP-MS. However, after seven days and 14 days of culture, the cells present fibroblastoid morphology, phenotype expected by this cellular type. The results give efforts to indicate this new material as a potential biomaterial for tissue engineering, in the future in vivo approach.
Abstract: The aim of this study is the review of the management practices of sickle cell disease patients during pregnancy, as well as the maternal and neonatal outcome at Ampang Hospital, Selangor. The study consisted of a review of pregnant patients with sickle cell disease under follow up at the Hematology Clinic, Ampang Hospital over the last seven years to assess their management and maternal-fetal outcome. The results of the review show that Ampang Hospital is considered the public hematology centre for sickle cell disease and had successfully managed three pregnancies throughout the last seven years. Patients’ presentations, managements and maternal-fetal outcome were compared and reviewed for academic improvements. All three patients were seen very early in their pregnancy and had been given a regime of folic acid, antibiotics and thrombo-prophylactic drugs. Close monitoring of maternal and fetal well being was done by the hematologists and obstetricians. Among the patients, there were multiple admissions during the pregnancy for either a painful sickle cell bone crisis, haemolysis following an infection and anemia requiring phenotype- matched blood and exchange transfusions. Broad spectrum antibiotics coverage during and infection, hydration, pain management and venous-thrombolism prophylaxis were mandatory. The pregnancies managed to reach near term in the third trimester but all required emergency caesarean section for obstetric indications. All pregnancies resulted in live births with good fetal outcome. During post partum all were nursed closely in the high dependency units for further complications and were discharged well. Post partum follow up and contraception counseling was comprehensively given for future pregnancies. Sickle cell disease is uncommonly seen in the East, especially in the South East Asian region, yet more cases are seen in the current decade due to improved medical expertise and advance medical laboratory technologies. Pregnancy itself is a risk factor for sickle cell patients as increased thrombosis event and risk of infections can lead to multiple crisis, haemolysis, anemia and vaso-occlusive complications including eclampsia, cerebrovasular accidents and acute bone pain. Patients mostly require multiple blood product transfusions thus phenotype-matched blood is required to reduce the risk of alloimmunozation. Emphasizing the risks and complications in preconception counseling and establishing an ultimate pregnancy plan would probably reduce the risk of morbidity and mortality to the mother and unborn child. Early management for risk of infection, thromboembolic events and adequate hydration is mandatory. A holistic approach involving multidisciplinary team care between the hematologist, obstetricians, anesthetist, neonatologist and close nursing care for both mother and baby would ensure the best outcome. In conclusion, sickle cell disease by itself is a high risk medical condition and pregnancy would further amplify the risk. Thus, close monitoring with combine multidisciplinary care, counseling and educating the patients are crucial in achieving the safe outcome.
Abstract: Growing environmental and sustainability concerns have driven continual modernization of horticultural practices, especially for urban farming. Controlled environment and soilless production methods are increasing in popularity because of their efficient resource use and intensive cropping capabilities. However, some popular substrates used for hydroponic cultivation, particularly rock wool, represent a large environmental burden in regard to their manufacture and disposal. Substrate-less hydroponic systems are effective in producing short cropping cycle plants such as lettuce or herbs, but less information is available for the production of plants with larger root-systems and longer cropping times. Here, we investigated the viability of a hybrid aeroponic/nutrient film technique (AP/NFT) system for the cultivation of greenhouse tomatoes (Solanum lycopersicum ‘Panovy’). The plants grown in the AP/NFT system had a more compact phenotype, accumulated more Na+ and less P and S than the rock wool grown counterparts. Due to forced irrigation interruptions, we propose that the differences observed were cofounded by the differing severity of water-stress for plants with and without substrate. They may also be caused by a higher root zone temperature predominant in plants exposed to AP/NFT. However, leaf area, stem diameter, and number of trusses did not differ significantly. The same was found for leaf pigments and plant photosynthetic efficiency. Overall, the AP/NFT system appears to be viable for the production of greenhouse tomato, enabling the environment to be relieved by way of lessening rock wool usage.
Abstract: Prediction of perturbations after genetic manipulation
(especially gene knockout) is one of the important challenges in
systems biology. In this paper, a new algorithm is introduced that
integrates microarray data into the metabolic model. The algorithm
was used to study the change in the cell phenotype after knockout of
Gss gene in Escherichia coli BW25113. Algorithm implementation
indicated that gene deletion resulted in more activation of the
metabolic network. Growth yield was more and less regulating gene
were identified for mutant in comparison with the wild-type strain.
Abstract: Fluoroquinolones form the mainstay of therapy for the treatment of infections due to Salmonella enterica subsp. enterica. There is a complex interplay between several resistance mechanisms for quinolones and various fluoroquinolones discs, giving varying results, making detection and interpretation of fluoroquinolone resistance difficult. For detection of fluoroquinolone resistance in Salmonella ssp., we compared the use of pefloxacin and nalidixic acid discs as surrogate marker. Using MIC for ciprofloxacin as the gold standard, 43.5% of strains showed MIC as ≥1 μg/ml and were thus resistant to fluoroquinoloes. Based on the performance of nalidixic acid and pefloxacin discs as surrogate marker for ciprofloxacin resistance, both the discs could correctly detect all the resistant phenotypes; however, use of nalidixic acid disc showed false resistance in the majority of the sensitive phenotypes. We have also tested newer antimicrobial agents like cefixime, imipenem, tigecycline and azithromycin against Salmonella spp. Moreover, there was a comeback of susceptibility to older antimicrobials like ampicillin, chloramphenicol, and cotrimoxazole. We can also use cefixime, imipenem, tigecycline and azithromycin in the treatment of multidrug resistant S. typhi due to their high susceptibility.
Abstract: Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p
Abstract: The paper presents the results of the molecular
genetics analysis in sports research, with special emphasis to use
genetic information in diagnosing of motoric predispositions in Roma
boys from East Slovakia. The ability and move are the basic
characteristics of all living organisms. The phenotypes are influenced
by a combination of genetic and environmental factors. Genetic tests
differ in principle from the traditional motoric tests, because
the DNA of an individual does not change during life. The aim of
the presented study was to examine motion abilities and to determine
the frequency of ACTN3 (R577X) gene in Roma children. Genotype
data were obtained from 138 Roma and 155 Slovak boys from 7 to 15
years old. Children were investigated on physical performance level
in association with their genotype. Biological material for genetic
analyses comprised samples of buccal swabs. Genotypes were
determined using Real Time High resolution melting PCR method
(Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The
software allows creating reports of any analysis, where information
of the specific analysis, normalized and differential graphs and many
information of the samples are shown. Roma children of analyzed
group legged to non-Romany children at the same age in all the
compared tests. The % distribution of R and X alleles in Roma
children was different from controls. The frequency of XX genotype
was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX
genotype was 9.26% which is comparable to a frequency of an Indian
population. Data were analyzed with the ANOVA test.
Abstract: Natural antimicrobials are used to preserve foods that
can be found in plants, animals, and microorganisms. Antimicrobial
substances are natural or artificial agents that produced by
microorganisms or obtained semi/total chemical synthesis are used at
low concentrations to inhibit the growth of other microorganisms.
Food borne pathogens and spoilage microorganisms are inactivated
by the use of antagonistic microorganisms and their metabolites.
Yeasts can produce toxic proteins or glycoproteins (toxins) that cause
inhibition of sensitive bacteria and yeast species. Antimicrobial
substance producing phenotypes belonging different yeast genus
were isolated from different sources. Toxins secreted by many yeast
strains inhibiting the growth of other yeast strains. These strains show
antimicrobial activity, inhibiting the growth of mold and bacteria.
The effect of antimicrobial agents produced by yeasts can be
extremely fast, and therefore may be used in various treatment
procedures. Rapid inhibition of microorganisms is possibly caused by
microbial cell membrane lipopolysaccharide binding and in
activation (neutralization) effect. Antimicrobial agents inhibit the
target cells via different mechanisms of action.
Abstract: Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.
Abstract: Tumor cells have an invasive and metastatic phenotype
that is the main cause of death for cancer patients. Tumor
establishment and penetration consists of a series of complex
processes involving multiple changes in gene expression. In this study,
intraperitoneal administration of a high concentration of ascorbic acid
inhibited tumor establishment and decreased tumor mass in BALB/C
mice implanted with S-180 sarcoma cancer cells. To identify proteins
involved in the ascorbic acid-mediated inhibition of tumor
progression, changes in the tumor proteome associated with ascorbic
acid treatment of BALB/C mice implanted with S-180 were
investigated using two-dimensional gel electrophoresis and mass
spectrometry. Twenty protein spots were identified whose expression
was different between control and ascorbic acid treatment groups.
Abstract: This research studied the simulation of increased
ambient ozone to estimate nutrient content and genetic changes in
two Thai soybean cultivars (Chiang Mai 60 and Srisumrong 1).
Ozone stress conditions affected proteins and lipids. It was found
that proteins decreased, but lipids increased. Srisumrong 1 cultivars
were more sensitive to ozone stress than Chiang Mai 60 cultivars.
The effect of ozone stress conditions on plant phenotype and
genotype was analyzed using the AFLP technique for the 2 Thai
soybean cultivars (Chiang Mai 60 and Srisumrong 1).
Abstract: Epstein-Barr virus (EBV) is implicated in the pathogenesis of the endemic Burkitt-s lymphoma (BL). The EBVpositive BL-derived cell lines initially maintain the original tumor phenotype of EBV infection (latency I, LatI), but most of them drift toward a lymphoblast phenotype of EBV latency III (LatIII) during in vitro culturing. The aim of the present work was to characterize the B-cell subsets in EBV-positive BL cell lines and to verify whether a particular cell subset correlates with the type of EBV infection. The phenotype analysis of two EBV-negative and eleven EBV-positive (three of LatI and eight of LatIII) BL cell lines was performed by polychromatic flow cytomery, based on expression pattern of CD19, CD10, CD38, CD27, and CD5 markers. Two cell subsets, CD19+CD10+ and CD19+CD10-, were defined in LatIII BL cell lines. In both subsets, the CD27 and CD5 cell surface expression was detected in a proportion of the cells.
Abstract: There is a world-wide need for the development of sustainable management strategies to control pest infestation and the development of phosphine (PH3) resistance in lesser grain borer (Rhyzopertha dominica). Computer simulation models can provide a relatively fast, safe and inexpensive way to weigh the merits of various management options. However, the usefulness of simulation models relies on the accurate estimation of important model parameters, such as mortality. Concentration and time of exposure are both important in determining mortality in response to a toxic agent. Recent research indicated the existence of two resistance phenotypes in R. dominica in Australia, weak and strong, and revealed that the presence of resistance alleles at two loci confers strong resistance, thus motivating the construction of a two-locus model of resistance. Experimental data sets on purified pest strains, each corresponding to a single genotype of our two-locus model, were also available. Hence it became possible to explicitly include mortalities of the different genotypes in the model. In this paper we described how we used two generalized linear models (GLM), probit and logistic models, to fit the available experimental data sets. We used a direct algebraic approach generalized inverse matrix technique, rather than the traditional maximum likelihood estimation, to estimate the model parameters. The results show that both probit and logistic models fit the data sets well but the former is much better in terms of small least squares (numerical) errors. Meanwhile, the generalized inverse matrix technique achieved similar accuracy results to those from the maximum likelihood estimation, but is less time consuming and computationally demanding.
Abstract: Human genome is not only the evolutionary
summation of all advantageous events, but also houses lesions of
deleterious foot prints. A single gene mutation sometimes may
express multiple consequences in numerous tissues and a linear
relationship of the genotype and the phenotype may often be obscure.
ß Thalassemia minor, a transfusion independent mild anaemia,
coupled with environment among other factors may articulate into
phenotypic pleotropy with Hypocholesterolemia, Vitamin D
deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological
alterations. Occurrence of Pancreatic insufficiency, resultant
steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with
Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor
patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2
4.60% and Hb Adult 84.80% and altered Hemogram) with increased
Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2
(9.5mg/ml) indicate towards a cascade of phenotypic pleotropy
where the ß Thalassemia mutation ,be it in the 5’ cap site of the
mRNA , differential splicing etc in heterozygous state is effecting
several metabolic pathways. Compensatory extramedulary
hematopoiesis may not coped up well with the stressful life style of
the young individual and increased erythropoietic stress with high
demand for cholesterol for RBC membrane synthesis may have
resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia
may have caused the pancreatic insufficiency, leading to Vitamin D
deficiency. This may in turn have caused the secondary
hyperparathyroidism to sustain serum Calcium level. Irritability and
stress intolerance of the patient was a cumulative effect of the vicious
cycle of metabolic compromises. From these findings we propose
that the metabolic deficiencies in the ß Thalassemia mutations may
be considered as the phenotypic display of the pleotropy to explain
the genetic epidemiology.
According to the recommendations from the NIH Workshop on
Gene-Environment Interplay in Common Complex Diseases: Forging
an Integrative Model, study design of observations should be
informed by gene-environment hypotheses and results of a study
(genetic diseases) should be published to inform future hypotheses.
Variety of approaches is needed to capture data on all possible
aspects, each of which is likely to contribute to the etiology of
disease. Speakers also agreed that there is a need for development of
new statistical methods and measurement tools to appraise
information that may be missed out by conventional method where
large sample size is needed to segregate considerable effect.
A meta analytic cohort study in future may bring about significant
insight on to the title comment.
Abstract: Phytases (myo-inositol hexakisphosphate
phosphohydrolases; EC 3.1.3.8) catalyze the hydrolysis of phytic acid
(myoinositol hexakisphosphate) to the mono-, di-, tri-, tetra-, and
pentaphosphates of myo-inositol and inorganic phosphate.
Therrmophilic bacteria isolated from water sampled from hot spring.
About 120 isolates of bacteria were successfully isolated form hot
spring water sample and tested for extracellular phytase producing.
After 5 passages of the screening on the PSM media, 4 isolates were
found stable in producing phytase enzyme. The 16s RDNA
sequencing for identification of bacteria using molecular technique
revealed that all isolates those positive in phytase producing are
belong to Geobacillus spp. And Anoxybacillus spp. Anoxybacillus
rupiensis UniSZA-7 were identified for their carbon source utilization
using Phenotype Microarray Plate of Biolog and found they utilize
several kind of carbon source provided.
Abstract: The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower
Abstract: An influence of intranasal combined injection of live
cold-adapted influenza vaccine with chitosan derivatives as adjuvants
on the subpopulation structure of mononuclear leukocytes of mouse
spleen which reflects the orientation of the immune response was
studied. It is found that the inclusion of chitosan preparations
promotes activation of cellular-level of immune response.
Abstract: Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Abstract: COPD is characterized by loss of elastic fibers from
small airways and alveolar walls, with the decrease in elastin
increasing with disease severity. It is unclear why there is a lack of
repair of elastic fibers. We have examined fibroblasts cultured from
lung tissue from normal and COPD subjects to determine if the
secretory profile explains lack of tissue repair. In this study,
fibroblasts were cultured from lung parenchyma of bronchial
carcinoma patients with varying degrees of COPD; controls
(non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe
COPD (GOLD 2-3, n=12). Measurements were made of proliferation,
senescence-associated beta-galactosidase-1, mRNA expression of
IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for
IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was
found that GOLD 2-3 fibroblasts proliferated more slowly (p