Grace Mccormack

• Doctor of Philosophy
• Professor at Ollscoil na Gaillimhe – University of Galway

Octocorals are sessile invertebrates that play a key role in marine habitats, with significant diversity in the Tropical Eastern Pacific, especially in Ecuador’s shallow waters. This study focuses on the most representative octocorals within the Marine Protected Area El Pelado, Santa Elena, Ecuador, as a part of a marine biodiscovery project employ...

The first taxonomic descriptions of the sponge diversity at El Pelado Marine Protected Area in the province of Santa Elena, Ecuador is reported. Tedania (Tedania) ecuadoriensis Jaramillo & Hajdu, sp. nov. is described from its shallow waters. In addition, Callyspongia (Callyspongia) aff. californica (sensu Cruz-Barraza and Carballo 2008; non sensu...

Apis mellifera mellifera (Linnaeus), the Western European honey bee, is considered extinct in the wild over most of its range due largely to hybridisation and replacement by other subspecies, parasitism by Varroa destructor, habitat loss, and effects from agricultural pesticides. The purity of the subspecies within the managed cohort is also at ris...

Honey bee abdominal pigmentation is one of the most recognisable traits and it is often used by beekeepers as an indicator of M-lineage subspecies purity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and the genetic background. To assess whether this trait...

This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six...

The shape and arrangement of skeletal structures (spicules) in marine sponges are used in their taxonomic classification but shared spicule patterns often do not correspond to relationships postulated by molecular data, particularly for members of the order Haplosclerida. A chemical and spectroscopic analysis of spicules using FTIR-ATR (Fourier tra...

This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six...

The emergence of antibiotic resistance and viruses with high epidemic potential made unexplored marine environments an appealing target source for new metabolites. Marine fungi represent one of the most suitable sources for the discovery of new compounds. Thus, the aim of this work was (i) to isolate and identify fungi associated with the Atlantic...

Silicatein is the main protein responsible for the formation of spicules, tiny structures that constitute the silica skeleton of marine demosponges (Phylum Porifera). A unique innovation in Porifera that evolved from the cathepsin L family of proteins, it has been reported that two amino acids (S and H) are necessary to form the catalytic triad (SH...

The skeletons of sponges (Phylum Porifera) are comprised of collagen, often embedded with small siliceous structures (spicules) arranged in various forms to provide strength and flexibility. The main proteins responsible for the formation of the spicules in demosponges are the silicateins, which are related to the cathepsins L of other animals. Whi...

Describing the use of mitochondrial, microsatellite and SNPs genotyping to characterise wild or feral or free-living honey bees in Ireland to determine both lineage and the level of introgression from C-lineage imports

The genus Hymeraphia currently comprises three species and all records of the genus are from the northeast Atlantic and the Mediterranean Sea. The present paper describes a new species, H. vaceleti sp. nov. from a deep-water canyon, off southwest Ireland. H. vaceleti sp. nov. is morphologically distinct from other Hymeraphia species and 28S rRNA se...

The natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A...

The natural range of the dark European honey bee, Apis mellifera mellifera has been significantly reduced in recent years as a result of importation and replacement of queens with those of other Apis subspecies. Previous studies have indicated that a substantial amount of A. m. mellifera populations throughout Europe are heavily hybridized but that...

Zoantharians represent a group of marine invertebrates widely distributed from shallow waters to the deep sea. Despite a high diversity and abundance in the rocky reefs of the Pacific Ocean, very few studies have been reported on the diversity of this group in the Tropical Eastern Pacific coasts. While molecular techniques recently clarified some t...

In October 2016, a rapid assessment survey of ascidian species was conducted in shellfish farms at Killary Fjord, in the west of Ireland. Two non-indigenous solitary ascidians Ascidiella aspersa and Corella eumoyta were recorded for the first time in shellfish farms at this location. Both invasive ascidians have the potential to greatly reduce muss...

We live in a time of concern regarding predicted environmental damage due to climate change, i.e. sea temperature increase and a reduction in ocean pH. Such changes will have severe consequences for at least some marine organisms. Developments in molecular and genomic techniques allow for genome-wide comparisons of genes and proteins that may be im...

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of spon...

The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome P...

Sponges and their associated microbiota are well known to produce a large diversity of natural products, also called specialized metabolites. In addition to their potential use in the pharmaceutical industry, these rather species-specific compounds may help in the classification of some particular sponge groups. We review herein compounds isolated...

Importance: The entry-inhibitor drug maraviroc makes the cell coreceptor CCR5 unavailable for use by HIV-1 and is now used in combination antiretroviral therapy. Treatment failure with drug resistant virus is particularly interesting because it tends to be rare with lack of sensitivity usually associated with the presence of CXCR4-using virus (the...

Antifungal bioactivity-guided fractionation of the organic extract of the sponge Polymastia boletiformis, collected from the west coast of Ireland, led to the isolation of two new sulfated steroid-amino acid conjugates (1 and 2). Extensive 1D and 2D NMR analyses in combination with quantum mechanical calculations of the electronic circular dichrois...

Antifungal bioactivity-guided fractionation of the organic extract of the sponge Polymastia boletiformis, collected from the west coast of Ireland, led to the isolation of two new sulfated steroid-amino acid conjugates (1 and 2). Extensive 1D and 2D NMR analyses in combination with quantum mechanical calculations of the electronic circular dichrois...

There are few cohorts of individuals, who have survived infection with HIV-1 for more than 20 years, reported and followed in the literature, and even fewer from Africa. Here we present data on a cohort of subtype C-infected individuals from rural northern Malawi. By sequencing multiple clones from long-term survivors at different time-points, and...

Many high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a sequence read. Undertaking quality trimming of this data is essential to enable confidence in the results of subsequent downstream analysis....

We provide a detailed, comparative study of the ciliated cells of the marine haplosclerid sponge Haliclona indistincta, in order to make data available for future phylogenetic comparisons at the ultrastructural level. Our study focuses on the description and analysis of the larval epithelial cells, and choanocytes of the metamorphosed juvenile spon...

In 2009, the Marine Biodiscovery Laboratory was set-up at the Marine Institute with funds from the Marine Institute and the Beaufort Marine Biodiscovery Research Programme. The Marine Biodiscovery Laboratory has already processed over 130 marine specimens from coastal zones and from the Deep Sea (<3,000 m) within the Marine Irish Exclusive Economic...

Haliclona indistincta has in some respects, a typical reproductive cycle for a marine haplosclerid sponge. We suggest that oocytes originate from archaeocytes and that spermatozoa originate from choanocytes. Oocytes were first seen in November and matured as eggs by May and June. Immature spermatic cysts were identified from February and mature cys...

It is well accepted that the freshwater sponges (Porifera; Haplosclerida; Spongillina) currently comprise six extant families: Spongillidae, Lubomirskiidae, Malawispongiidae, Metaniidae, Metschnikowiidae and Potamolepidae, but the phylogeny of this group is poorly understood. Family Malawispongiidae includes five genera: Malawispongia, Spinospongil...

Although interactions between seaweeds and sponges have been studied in detail, general information concerning the whole epibiontic algal assemblage associated with a sponge species is virtually non-existent. We present here the first study in which the macroalgal community associated with a sponge, Haliclona indistincta (Bowerbank), was examined i...

Background The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary focus of this work was to characterize the genetic diversity and evolution of HIV drug resistant variants in an individual’s provirus d...

ABSTRACT: Drug resistance testing before initiation of, or during, antiretroviral therapy (ART) is not routinely performed in resource-limited settings. High levels of viral resistance circulating within the population will have impact on treatment programs by increasing the chances of transmission of resistant strains and treatment failure. Here,...

Maximum-likelihood phylogeny reconstructed from the D3-D5 region of the 28S rRNA gene. The DNA substitution model parameters by RAxML were; f(A) 0.23, f(C) 0.24, f(G) 0.32, f(T) 0.21; R(AC) 0.57, R(AG) 2.03, R(AAT) 1.0, R(CG) 0.57, R(CT) 4.19, R(GT) 1.0; alpha 0.19. Sequences produced during this study are in bold. Sampling locations for each taxon...

Maximum-likelihood phylogeny reconstructed from the Folmer (5′) region of the cox1 gene. The DNA substitution model parameters estimated by RAxML were; f(A) 0.26, f(C) 0.15, f(G) 0.22, f(T) 0.37; R(AC) 1.37, R(AG) 4.1, R(AT) 1.43, R(CG) 1.18, R(CT) 6.87, R(GT) 1.0; alpha 0.71; pinvar 0.41. Sequences produced during this study are in bold. Sampling...

Maximum-likelihood phylogeny reconstructed from the nad1 gene. The DNA substitution model parameters by RAxML were; f(A) 0.3, f(C) 0.1, f(G) 0.21, f(T) 0.39; R(AC) 4.18, R(AG) 6.72, R(AT) 1.0, R(CG) 4.18, R(CT) 11.9, R(GT) 1.0; alpha 0.26; pinvar 0.08. Sequences produced during this study are in bold. Sampling locations for each taxon are given in...

List of all the marine haplosclerid specimens sequenced in this study. Sampling location, voucher number where available, and what gene regions were sequenced for each is included. (DOC)

Primer sequence information for each primer used in amplifying each gene region. (DOC)

The final D3 alignment used for analysis. (NEX)

The concatenated dataset created by joining sequences of the D1 and D3–D5 regions from specimens that had both regions available. (NEX)

The cox1 dataset including sequences from only Haplosclerida. (NEX)

The final D1 alignment used for analysis. (NEX)

The cox1 dataset including sequences from other demospnge orders and cnidarians. (NEX)

The nad1 alignment used for analysis. (NEX)

The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across...

In this study, for the first time the diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis collected from the Sousern Basin of Lake Baikal was investigated employing cultivation-independent approaches. In total, 102 bacterial 16S rRNA clones were screened using restriction fragment length polymorphism (RFLP) a...

Here we present new sequence data from HIV-1 subtype C-infected long-term survivors (LTS) from Karonga District, Malawi. Gag and env sequence data were produced from nine individuals each of whom has been HIV-1 positive for more than 20 years. We show that the three amino acid deletion in gag p17 previously described from these LTS is not real and...

Binding to a chemokine receptor, either CCR5 or CXCR4, by the gp120 glycoprotein is an essential step in the pathway by which HIV enters host cells. Recently, CCR5 antagonists have been developed that obstruct binding of CCR5 by gp120, thus inhibiting host cell entry. Resistance to such CCR5 antagonists may emerge, however, through the selection of...

In this preliminary study we show that in 2008, 3 years after antiretroviral therapy was introduced into the Karonga District, Malawi, a greater than expected number of drug-naive individuals have been infected with HIV-1 subtype C virus harboring major and minor drug resistance mutations (DRMs). From a sample size of 40 reverse transcriptase (RT)...

Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equival...

Taxonomy within the sponge Order Haplosclerida remains somewhat contentious. Both morphology and biochemistry have been employed to help unravel the relationships of the Order with limited results perhaps because of the small number of reliable characters. We employed phylogenetic analysis of 750 base pairs of the 5′ end of the 28S rRNA gene to stu...

Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have three large indels in the 18S r...

The env gene of human immunodeficiency virus (HIV) is a functionally important gene responsible for the production of protein products (gp120 and gp41) involved in host cell recognition, binding, and entry. This occurs through a complex and, as yet, not fully understood process of protein-protein interaction and within and between protein functiona...

A minute bivalve, Adontorhina keegani, new species (Thyasiridae) is described from the Porcupine Bank, west of Ire- land. The new species occurs between 300 and 789 m on the continental slope. The shell is elongate and compressed, with a flattened posterior and complete lack of radial sulcus. The shell has a hinge margin bearing irregular granules...

A minute bivalve, Adontorhina keegani, new species (Thyasiridae) is described from the Porcupine Bank, west of Ireland. The new species occurs between 300 and 789 m on the continental slope. The shell is elongate and compressed, with a flattened posterior and complete lack of radial sulcus. The shell has a hinge margin bearing irregular granules an...

In animal olfactory systems, odorant molecules are detected by olfactory receptors (ORs). ORs are part of the G-protein-coupled receptor (GPCR) superfamily. Heterotrimeric guanine nucleotide binding G-proteins (G-proteins) relay signals from GPCRs to intracellular effectors. G-proteins are comprised of three peptides. The G-protein alpha subunit co...

The validity of Pseudocuma gilsoni Bǎcescu 1950 has been questioned in the past. The recent discovery of material in Irish waters, and in the North Sea, confirms the presence of the species in the North East Atlantic and provides the opportunity to present a full redescription. A new genus, Monopseudocuma, is erected to accommodate the species. A n...

Hematopoietic stem cell transplant recipients frequently develop BK virus (BKV)-associated hemorrhagic cystitis, which coincides with BK viruria. However, the precise role of BKV in the etiology of hemorrhagic cystitis in hematopoietic stem cell transplant recipients remains unclear, since approximately 50% of all such adult transplant recipients e...

In a population-based study in northern Malawi we investigated HIV-1 subtype C gag and env gene sequences associated with long-term survival. DNA samples were available from 31 individuals surviving between population surveys carried out in the 1980s and 1990s. Most survivors with paired sequences dating from the 1980s and the 1990s had a three cod...

This molecular phylogenetic analysis of 18S ribosomal RNA (18SrDNA) gene sequences from 16 species of holothuroid, suggests strong support for an alternative taxonomic scheme to replace the existing classification. When trees drawn from the 18S rDNA data were constrained to show expected relationships between the holothourid orders, they were signi...

Human metapneumovirus (hMPV) is a newly identified paramyxovirus that has been associated with respiratory tract illness in children aged < 5 years, the elderly, and immunocompromised patients. This study determined the frequency of respiratory tract infections (RTIs) associated with hMPV in the Republic of Ireland. Bronchoalveolar lavage (BAL) sam...

Motivation: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to addr...

Recent studies have demonstrated the emergence of human immunodeficiency virus type 1 (HIV-1) subtypes with various levels of fitness. Using heterogeneous maximum-likelihood models of adaptive evolution implemented in the PAML software package, with env sequences representing each HIV-1 group M subtype, we examined the various intersubtype selectiv...

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from th...

The astigmatid mite Acarus siro (Linnaeus 1758) is an important agricultural pest and environmental allergen. However, it is likely that many mites described in the literature as A. siro, collected from both outdoor and stored product habitats, may belong to one of its sibling species, A. farris [Ent. Ber. Amst. 2 (26) (1905) 20] or A. immobilis [B...

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP,...