Nora Khaldi

Nora Khaldi
University College Dublin | UCD · Conway Institute of Biomolecular & Biomedical Research

About

61
Publications
6,666
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2,065
Citations
Introduction
Additional affiliations
December 2011 - February 2012
Position
  • University College Davis
January 2008 - present
University College Dublin
December 2004 - June 2008
Trinity College Dublin

Publications

Publications (61)
Article
Full-text available
Scientific research consistently demonstrates that diseases may be delayed, treated, or even prevented and, thereby, health may be maintained with health-promoting functional food ingredients (FFIs). Consumers are increasingly demanding sound information about food, nutrition, nutrients, and their associated health benefits. Consequently, a nutriti...
Article
Full-text available
Fresh-cut fruits and vegetables are becoming particularly popular as healthy fast-food options; however, they present challenges such as accelerated rates of decay and increased risk for contamination when compared to whole produce. Given that food safety must remain paramount for producers and manufacturers, research into novel, natural food prese...
Article
Full-text available
The prevalence of prediabetes is rapidly increasing, and this can lead to an increased risk for individuals to develop type 2 diabetes and associated diseases. Therefore, it is necessary to develop nutritional strategies to maintain healthy glucose levels and prevent glucose metabolism dysregulation in the general population. Functional ingredients...
Article
Full-text available
Characterising key components within functional ingredients and assessing efficacy and bioavailability is an important step in validating nutritional interventions. Machine learning can assess large and complex data sets, such proteomic data from plants sources, and so offers a prime opportunity to predict key active components within a larger matr...
Article
Full-text available
While there have been significant advances in drug discovery for diabetes mellitus over the past couple of decades, there is an opportunity and need for improved therapies. While type 2 diabetic patients better manage their illness, many of the therapeutics in this area are peptide hormones with lengthy sequences and a molecular structure that make...
Article
Full-text available
Bioactive peptides are known to have many health benefits beyond nutrition; yet the peptide profile of high protein ingredients has been largely overlooked when considering the effects of different processing techniques. Therefore, to investigate whether drying conditions could affect the peptide profile and bioactivity within a functional ingredie...
Article
Full-text available
Food-derived bioactive peptides offer great potential for the treatment and maintenance of various health conditions, including chronic inflammation. Using in vitro testing in human macrophages, a rice derived functional ingredient natural peptide network (NPN) significantly reduced Tumour Necrosis Factor (TNF)-α secretion in response to lipopolysa...
Article
Full-text available
Bovine-derived formula milk (FM) is a common substitute to human milk (HM), but lacks key functional benefits associated with HM. Accordingly there have been significant efforts to humanise FM. Recent research has demonstrated that HM-derived peptides convey an array of beneficial bioactivities. Given that peptides serve as important signalling mol...
Article
Full-text available
Little is known about the digestive process in infants. In particular, the chronological activity of enzymes across the course of digestion in the infant remains largely unknown. To create a temporal picture of how milk proteins are digested, enzyme activity was compared between intact human milk samples from three mothers and the gastric samples f...
Article
Full-text available
In vitro digestion of isolated milk proteins results in milk peptides with a variety of actions. However, it remains unclear to what degree protein degradation occurs in vivo in the infant stomach and whether peptides previously annotated for bioactivity are released. This study combined nanospray liquid chromatography separation with time-of-fligh...
Article
Full-text available
Human milk is known to contain several proteases, but little is known about whether these enzymes are active, which proteins they cleave and their relative contribution to milk protein digestion in vivo. We analyzed the mass spectrometry-identified protein fragments found in pooled human milk by comparing their cleavage sites with the enzyme specif...
Article
This study used bioinformatics to mine the five major milk proteins for angiotensin converting enzyme- (ACE-) inhibitor peptides. We found three ACE-inhibitors, two of which were novel (QSWMHQPHQ and YYAKPAAVR). Peptides QSWMHQPHQ and YYAKPAAVR dose-dependently increased ACE inhibition with IC50 values of 19.26 and 48.88 μm, respectively. RAW 264.7...
Article
Milk is a hallmark of mammalian evolution: a unique food that has evolved with mammals. Despite the importance of this food, it is not known if variation in AA composition between different species is important to milk proteins or how it might affect the nutritional value of milk. As milk is the only food source for newborn mammals, it has long bee...
Article
With the continued progression of the “omics” era, bioinformatics, a discipline concerned with the curation and interpretation of biological data by computational means, has seen widespread integration across life sciences. However, despite becoming very data rich disciplines in the past number of years, the role of bioinformatics in food and nutri...
Article
Full-text available
Milk is traditionally considered an ideal source of the basic elemental nutrients required by infants. More detailed examination is revealing that milk represents a more functional ensemble of components with benefits to both infants and mothers. A comprehensive peptidomics method was developed and used to analyze human milk yielding an extensive a...
Article
Mass spectrometric analysis of peptides contained in enzymatically digested hydrolysates of proteins is increasingly being used to characterize potentially bioactive or otherwise interesting hydrolysates. However, when preparations containing mixtures of enzymes are used, from either biological or experimental sources, it is unclear which of these...
Article
Full-text available
The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable produ...
Article
Full-text available
Intracellular juxtamembrane regions of transmembrane proteins play pivotal roles in cell signalling, mediated by protein-protein interactions. Disordered protein regions, and short conserved motifs within them, are emerging as key determinants of many such interactions. Here, we investigated whether disorder and conserved motifs are enriched in the...
Data
Distribution of experimentally characterized motifs from the Eukaryotic Linear Motif (ELM) database on the intracellular regions of transmembrane proteins. Only proteins with intracellular regions greater than 150 amino acids in length were used. (TIFF)
Data
Amino acid composition of disordered residues. (TIFF)
Data
Conserved motifs in the cytoplasmic tails of single-pass transmembrane proteins. A conservative threshold of 1E-04 was used. (DOC)
Data
List of proteins with predicted conserved motif in the juxtamembrane region. (DOC)
Data
Protein dataset used in the present study. (DOC)
Data
Mean IUPred disorder profile (in red) for residues from 803 human single-pass transmembrane proteins, with respect to distance from the membrane. (position 0; extracellular negative, intracellular positive). The membrane region was not included in the analysis, and has been omitted from the graph. Standard errors are displayed in yellow. The number...
Data
Equations used in the calculation of Relative Local Conservation and the estimation of motif probability. (DOC)
Article
Protein disorder has been frequently associated with protein-protein interaction. However, our knowledge of how protein disorder evolves within a network is limited. It is expected that physically interacting proteins evolve in a coordinated manner. This has so far been shown in their evolutionary rate, and in their gene expression levels. Here we...
Data
Listing of the singletons in S. cerevisiae, their orthologs in L. kluyveri, and their corresponding intrinsically disordered regions classified into the three scenarios represented in figure 1. Proteins that have undergone only one scenario, for example a gain of a new intrinsically disordered region, have 1 or more intrinsic disorder in scenario,...
Data
Full-text available
Listing of the ohnologs in S. cerevisiae, their orthologs in L. kluyveri, and their corresponding intrinsically disordered regions classified into the four scenarios represented in Figure 1. Proteins that have undergone only one scenario, for example a gain of a new intrinsically disordered region, have 1 or more intrinsically disordered region in...
Article
Full-text available
Intrinsically disordered regions are enriched in short interaction motifs that play a critical role in many protein-protein interactions. Since new short interaction motifs may easily evolve, they have the potential to rapidly change protein interactions and cellular signaling. In this work we examined the dynamics of gain and loss of intrinsically...
Data
Table S1. Threshold for large pI shifts between all the mammals and human. Each row contains the name of the species, the threshold above which a shift in pI is considered as important, and finally the number of proteins that satisfy the difference in pI.
Article
Full-text available
Milk proteins are required to proceed through a variety of conditions of radically varying pH, which are not identical across mammalian digestive systems. We wished to investigate if the shifts in these requirements have resulted in marked changes in the isoelectric point and charge of milk proteins during evolution. We investigated nine major milk...
Article
Full-text available
The secondary metabolite gene clusters of euascomycete fungi are among the largest known clusters of functionally related genes in eukaryotes. Most of these clusters are species specific or genus specific, and little is known about how they are formed during evolution. We used a comparative genomics approach to study the evolutionary origins of a s...
Data
Full-text available
Maximum likelihood trees for the common fumonisin proteins between F. verticillioides and A. niger and their homologs. The species name and the NCBI ID are provided on each branch. Bootstrap percentages are shown for all nodes. Trees were constructed from amino acid sequences as described in Methods using PHYML after alignment with ClustalW.
Article
Although important shifts in the isoelectric point of prokaryotic proteins, mainly due to adaptation to environmental pH, have been widely reported, such studies have not covered mammalian proteins, where pH changes may relate to changes in subcellular or tissue compartmentalization. We explored the isoelectric point of the proteome of 13 mammalian...
Article
Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics and pharmaceuticals. The genes responsible for their biosynthesis, export, and transcriptional regulation are often found in contiguous gene clusters. To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based s...
Data
Names and putative functions of A. oryzae gene pairs showing Topologies A, B or C. (0.03 MB DOC)
Article
Full-text available
We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core,...
Data
Growth rates of Af293, A1163, N. fischeri, and A. clavatus isolates at various temperatures. (0.02 MB XLS)
Data
Five A. fumigatus loci exhibiting trans-species polymorphism. (0.02 MB XLS)
Data
Features of A. fumigatus-specific genes. (0.02 MB XLS)
Data
Enzymes that control the first step in secondary metabolite biosynthesis. (0.02 MB XLS)
Data
Allergens and sexual development genes. (0.05 MB DOC)
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Selective constraints operating on virulence-associated genes. (0.02 MB XLS)
Data
Known A. fumigatus Af293 allergens. (0.02 MB XLS)
Data
Fungal genomes used in phylogenetic analyses. (0.02 MB XLS)
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A. fumigatus core and species-specific genes. (0.02 MB XLS)
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Top PFAM domains overrepresented among four lineage specificity groups. (0.02 MB XLS)
Data
Resistance to antifungals among A. fumigatus clinical isolates. (0.02 MB XLS)
Data
Divergent A. fumigatus Af293 genes with respect to Af294, Af71, and A1163. (0.03 MB XLS)
Data
Distribution of polymorphic alleles among A. fumigatus isolates. (0.02 MB XLS)
Data
Top biological processes overrepresented among four lineage specificity groups. (0.02 MB XLS)
Data
Lineage specificity and chromosomal location. (0.02 MB XLS)
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Selective constraints operating on sex genes. (0.02 MB XLS)
Data
Families of transposable elements identified in the Affc genomes. (0.01 MB XLS)
Data
Predicted A. fumigatus Af293 allergens. (0.02 MB XLS)
Article
Full-text available
The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulan...
Article
Full-text available
Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular conditions. Such secondary metabolism gene clusters evolve rapidly through multiple rearrangements, duplications and losses. It has long been s...

Projects

Project (1)