Unlocking ground-based imagery for habitat mapping

Fine-grained environmental data across large extents are needed to resolve the processes that impact species communities from local to global scales. Ground-based images (GBIs) have the potential to capture habitat complexity at biologically relevant spatial and temporal resolutions. Moving beyond existing applications of GBIs for species identification and monitoring ecological change from repeat photography, we describe promising approaches to habitat mapping, leveraging multimodal data and computer vision. We illustrate empirically how GBIs can be applied to predict distributions of species at fine scales along Street View routes, or to automatically classify and quantify habitat features. Further, we outline future research avenues using GBIs that can bring a leap forward in analyses for ecology and conservation with this underused resource.

Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm

The trunk axial skeleton develops from paraxial mesoderm cells. Our recent study demonstrated that conditional knockout of the stem cell factor Sall4 in mice by TCre caused tail truncation and a disorganized axial skeleton posterior to the lumbar level. Based on this phenotype, we hypothesized that, in addition to the previously reported role of Sall4 in neuromesodermal progenitors, Sall4 is involved in the development of the paraxial mesoderm tissue. Analysis of gene expression and SALL4 binding suggests that Sall4 directly or indirectly regulates genes involved in presomitic mesoderm differentiation, somite formation and somite differentiation. Furthermore, ATAC-seq in TCre; Sall4 mutant posterior trunk mesoderm shows that Sall4 knockout reduces chromatin accessibility. We found that Sall4-dependent open chromatin status drives activation and repression of WNT signaling activators and repressors, respectively, to promote WNT signaling. Moreover, footprinting analysis of ATAC-seq data suggests that Sall4-dependent chromatin accessibility facilitates CTCF binding, which contributes to the repression of neural genes within the mesoderm. This study unveils multiple mechanisms by which Sall4 regulates paraxial mesoderm development by directing activation of mesodermal genes and repression of neural genes.

Sall genes regulate hindlimb initiation in mouse embryos

Vertebrate limbs start to develop as paired protrusions from the lateral plate mesoderm at specific locations of the body with forelimb buds developing anteriorly and hindlimb buds posteriorly. During the initiation process, limb progenitor cells maintain active proliferation to form protrusions and start to express Fgf10, which trigger molecular processes for outgrowth and patterning. Although both processes occur in both types of limbs, forelimbs (Tbx5) and hindlimbs (Isl1) utilize distinct transcriptional systems to trigger their development. Here, we report that Sall1 and Sall4, zinc finger transcription factor genes, regulate hindlimb initiation in mouse embryos. Compared to the 100% frequency loss of hindlimb buds in TCre; Isl1 conditional knockouts, Hoxb6Cre; Isl1 conditional knockout causes a hypomorphic phenotype with only approximately 5% of mutants lacking the hindlimb. Our previous study of SALL4 ChIP-seq showed SALL4 enrichment in an Isl1 enhancer, suggesting that SALL4 acts upstream of Isl1. Removing one allele Sall4 from the hypomorphic Hoxb6Cre; Isl1 mutant background caused loss of hindlimbs, but removing both alleles caused an even higher frequency of loss of hindlimbs, suggesting a genetic interaction between Sall4 and Isl1. Furthermore, TCre-mediated conditional double knockouts of Sall1 and Sall4 displayed a loss of expression of hindlimb progenitor markers (Isl1, Pitx1, Tbx4) and failed to develop hindlimbs, demonstrating functional redundancy between Sall1 and Sall4. Our data provides genetic evidence that Sall1 and Sall4 act as master regulators of hindlimb initiation.

Cis-regulatory control of mammalian Trps1 gene expression

TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.

Genomic Characterization of Low and High Grade Cervical Intraepithelial Neoplasia in Comparison to Cervical Cancer

PURPOSE/OBJECTIVE(S)

Screening reduces incidence of cervical cancer (CC) through identification and treatment of cervical intraepithelial neoplasia (CIN). Triage of CIN must balance between overtreatment versus progression as invasive therapies increase the risk of side effects including obstetric complications. The majority of CIN 1-2 lesions regress and a subset of CIN 3 lesions progress, however, due to inability to differentiate lesions likely to progress, the majority of CIN 2-3 lesions are treated with resection. Improved genomic and molecular identifiers of disease represent an urgent unmet clinical need.

MATERIALS/METHODS

Using next generation sequencing of a targeted exome panel of 1109 genes (previously validated), we characterized somatic mutations in 36 CIN (14 CIN 1, 11 CIN 2, 11 CIN 3) and 13 CC samples. Sequencing of CIN samples was performed on exfoliated cervical cells. CIN diagnosis and grade was confirmed on biopsy. Mutation profiles between CIN grades and CC were compared to identify genomic patterns that distinguish these groups.

RESULTS

Across the 49 samples sequenced, we identified a total of 5142 somatic mutations, including 2178 missense, 2522 synonymous, 171 nonsense, 62 splice site, 135 inframe indels, and 74 frameshift mutations. The mutation frequency was significantly higher in CC vs CIN1-3 (Table), p<0.01 (Wilcoxon signed-rank test). The difference in mutation frequency and type (Table) was not significant between CIN grades 1, 2 and 3 (p = 0.07, Kruskal-Wallis test). Cancer related pathway signatures were analyzed for the percentage of CC vs CIN samples with at least one altered variant as follows: RTK-RAS (92% vs 31%), PI3K (92% vs 17%), NOTCH (100% vs 39%), WNT (85% vs 14%) and cell cycle (53% vs 3%). Ninety percent of CC samples versus only 30% of CINs had nonsynonymous variants in the RTK-RAS and NOTCH pathways as well as the PI3K pathway which is implicated as a late event in cervical carcinogenesis. We observed recurrent missense variants in ABL1, IGF1R, TSC2 in the CIN2, CIN3 and CC samples, particularly in genes that belong to the RTK-RAS, PI3K, NOTCH pathway signatures. Potential driver mutations in EGFR, PIK3CA, ERBB4, MTOR, CSF1R genes were exclusive to CC samples.

CONCLUSION

Our results show that there is a clear distinction of mutational burden and type between cervical cancer and CIN1-3. However, the pathologic grading of CIN is not consistently associated with dynamic changes in overall mutation burden, type, or specific genes with escalating CIN grade. This data supports the hypothesis that late genetic events in CIN accompany a transition to invasive cervical cancer.

Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes

Recent studies illustrate the importance of regulation of cellular metabolism, especially glycolysis and pathways branching from glycolysis, during vertebrate embryo development. For example, glycolysis generates cellular energy ATP. Glucose carbons are also directed to the pentose phosphate pathway, which is needed to sustain anabolic processes in the rapidly growing embryos. However, our understanding of the exact status of glycolytic metabolism as well as genes that regulate glycolytic metabolism are still incomplete. Sall4 is a zinc finger transcription factor that is highly expressed in undifferentiated cells in developing mouse embryos, such as blastocysts and the post-implantation epiblast. TCre; Sall4 conditional knockout mouse embryos exhibit various defects in the posterior part of the body, including hindlimbs. Using transcriptomics approaches, we found that many genes encoding glycolytic enzymes are upregulated in the posterior trunk, including the hindlimb-forming region, of Sall4 conditional knockout mouse embryos. In situ hybridization and qRT-PCR also confirmed upregulation of expression of several glycolytic genes in hindlimb buds. A fraction of those genes are bound by SALL4 at the promoters, gene bodies or distantly-located regions, suggesting that Sall4 directly regulates expression of several glycolytic enzyme genes in hindlimb buds. To further gain insight into the metabolic status associated with the observed changes at the transcriptional level, we performed a comprehensive analysis of metabolite levels in limb buds in wild type and Sall4 conditional knockout embryos by high-resolution mass spectrometry. We found that the levels of metabolic intermediates of glycolysis are lower, but glycolytic end-products pyruvate and lactate did not exhibit differences in Sall4 conditional knockout hindlimb buds. The increased expression of glycolytic genes would have caused accelerated glycolytic flow, resulting in low levels of intermediates. This condition may have prevented intermediates from being re-directed to other pathways, such as the pentose phosphate pathway. Indeed, the change in glycolytic metabolite levels is associated with reduced levels of ATP and metabolites of the pentose phosphate pathway. To further test whether glycolysis regulates limb patterning downstream of Sall4, we conditionally inactivated Hk2, which encodes a rate-limiting enzyme gene in glycolysis and is regulated by Sall4. The TCre; Hk2 conditional knockout hindlimb exhibited a short femur, and a lack of tibia and anterior digits in hindlimbs, which are defects similarly found in the TCre; Sall4 conditional knockout. The similarity of skeletal defects in Sall4 mutants and Hk2 mutants suggests that regulation of glycolysis plays a role in hindlimb patterning. These data suggest that Sall4 restricts glycolysis in limb buds and contributes to patterning and regulation of glucose carbon flow during development of limb buds.

Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif

The Spalt-like 4 transcription factor (SALL4) plays an essential role in controlling the pluripotent property of embryonic stem cells via binding to AT-rich regions of genomic DNA, but structural details on this binding interaction have not been fully characterized. Here, we present crystal structures of the zinc finger cluster 4 (ZFC4) domain of SALL4 (SALL4ZFC4) bound with different dsDNAs containing a conserved AT-rich motif. In the structures, two zinc fingers of SALL4ZFC4 recognize an AATA tetranucleotide. We also solved the DNA-bound structures of SALL3ZFC4 and SALL4ZFC1. These structures illuminate a common preference for the AATA tetranucleotide shared by ZFC4 of SALL1, SALL3, and SALL4. Furthermore, our cell biology experiments demonstrate that the DNA-binding activity is essential for SALL4 function as DNA-binding defective mutants of mouse Sall4 failed to repress aberrant gene expression in Sall4-/- mESCs. Thus, these analyses provide new insights into the mechanisms of action underlying SALL family proteins in controlling cell fate via preferential targeting to AT-rich sites within genomic DNA during cell differentiation.

P–253 Description of a rare spontaneous monozygotic blastocyst splitting into two discrete euploid blastocysts in vitro detected with time-lapse imaging and preimplantation genetic testing (PGT)

Study question

Can spontaneous and complete blastocyst splitting into two, in vitro, be investigated using time-lapse imaging and biopsy of each trophectoderm, for inference of ploidy?

Summary answer

Time-lapse imaging combined with PGT-A gives insights into the incidence, dynamics and timing of rare blastocyst splitting and the ploidy status of each resulting blastocyst.

What is known already

It is well known that multiple births occur more often with Assisted Reproductive Technologies (ART) than spontaneous conception, even after single embryo transfer. The mechanism of Monozygotic Twinning (MZT) during ART is still unclear but cryopreservation, extended culture, PGT, maternal age and assisted hatching are reported risk factors. MZT is a rare phenomenon, with an incidence of 0.4% in natural conception compared with up to 4.9% in ART. The timing of embryo splitting dictates the type of twinning, in terms of chorionicity and amnionicty, and this is officially determined using ultrasound scanning.

Study design, size, duration

This is a case study describing the detection of the complete splitting of an IVF blastocyst at 140 hours post insemination (hpi), using time-lapse imaging.

The 40-year-old patient previously experienced biochemical pregnancy and several miscarriages; an ectopic molar pregnancy and a probable cornual ectopic. The 39-year-old male partner was normozoospermic.

Participants/materials, setting, methods

Facilitative laser breaching was performed, according to standard operating procedure, of the morula at 96hpi of embryo development, prior to PGT. Images were collected every 10 minutes and developmental events and embryos morphology annotated using the EmbryoScope+™ time lapse incubator and software.

Main results and the role of chance

Over 50,000 hatching blastocysts have been time-lapse imaged, scrutinised and annotated within this group of fertility clinics. This is the first time that such a rare blastocyst splitting event has been recorded and studied.

Following observation of two pronuclei following IVF and typical cleavage development to blastocyst, with facilitative zona breaching on, at 106.7hpi, the full blastocyst’s trophectoderm (TE) began to herniate and hatch. By 114.3hpi a second internal blastocoel cavity formed appearing to divide the inner cell mass (ICM) within the zona pellucida (ZP). This resulting blastocyst proceeded to hatch as its discrete ICM migrated out of the ZP, along with its TE. TE cells from the original blastocyst then began to hatch at 117.5hpi at the same breached site in the ZP with its ICM visibly evacuating the ZP.

By 140hpi the blastocyst had split into two discrete blastocysts while hatching from the ZP. Both resulting blastocysts had clear and separate ICMs and TEs present. Biopsy of approximately 5 cells was performed for each TE, and the blastocysts were vitrified individually. Next Generation Sequencing (NGS) reported both blastocysts to be euploid.

Limitations, reasons for caution

This case may have been detectable without time-lapse imaging, as the splitting was completed prior to biopsy. More expert scrutiny of the images may result in earlier signs of twinning in progress being detected.

Wider implications of the findings: The nature of this detectable in vitro blastocyst splitting, indicates these embryos (if they implanted) to be monozygotic, dichoriol-diamniotic ‘identical’ twins. However – as single embryo transfer is the preferred treatment plan; they may be born years apart. These observations could shed light on the debated models of monozygotic twinning.

Trial registration number

Not applicable

The effects of remote ischaemic preconditioning on coronary artery function in patients with stable coronary artery disease

Background

Remote ischaemic preconditioning (RIPC) is a cardioprotective intervention invoking intermittent periods of ischaemia in a tissue or organ remote from the heart. The mechanisms of this effect are incompletely understood. We hypothesised that RIPC might enhance coronary vasodilatation by an endothelium-dependent mechanism.

Methods

We performed a prospective, randomised, sham-controlled, blinded clinical trial. Patients with stable coronary artery disease (CAD) undergoing elective invasive management were prospectively enrolled, and randomised to RIPC or sham (1:1) prior to angiography. Endothelial-dependent vasodilator function was assessed in a non-target coronary artery with intracoronary infusion of incremental acetylcholine doses (10^− 6, 10^− 5, 10^− 4 mol/l). Venous blood was sampled pre- and post-RIPC or sham, and analysed for circulating markers of endothelial function. Coronary luminal diameter was assessed by quantitative coronary angiography. The primary outcome was the between-group difference in the mean percentage change in coronary luminal diameter following the maximal acetylcholine dose (Clinicaltrials.gov identifier: NCT02666235).

Results

75 patients were enrolled. Following angiography, 60 patients (mean ± SD age 57.5 ± 8.5 years; 80% male) were eligible and completed the protocol (n = 30 RIPC, n = 30 sham). The mean percentage change in coronary luminal diameter was − 13.3 ± 22.3% and − 2.0 ± 17.2% in the sham and RIPC groups respectively (difference 11.32%, 95%CI: 1.2– 21.4, p = 0.032). This remained significant when age and sex were included as covariates (difference 11.01%, 95%CI: 1.01– 21.0, p = 0.035). There were no between-group differences in endothelial-independent vasodilation, ECG parameters or circulating markers of endothelial function.

Conclusions

RIPC attenuates the extent of vasoconstriction induced by intracoronary acetylcholine infusion. This endothelium-dependent mechanism may contribute to the cardioprotective effects of RIPC.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry

BACKGROUND

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS.

AIMS

The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results.

SOURCES

Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed.

CONTENT

Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided.

IMPLICATIONS

Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner.

Development of nalidixic acid amphotericin B vancomycin (NAV) medium for the isolation of Campylobacter ureolyticus from the stools of patients presenting with acute gastroenteritis

Recently, Campylobacter ureolyticus has been detected for the first time in the faeces of patients with acute gastroenteritis using polymerase chain reaction (PCR) techniques. Cultural isolation of C. ureolyticusis is not possible using the established selective methods for the isolation of thermophilic Campylobacter spp. from faeces. The aim of the current study is to develop a new selective medium capable of isolating C. ureolyticus from faecal samples. The newly-developed medium consists of Anaerobe Basal Agar with 10 g/L additional agar, 2 g/L sodium formate and 3 g/L sodium fumarate dibasic, to which 10 mg/L nalidixic acid, 10 mg/L amphotericin B and 20 mg/L vancomycin (NAV) are added as selective agents. Validation studies have shown that this experimental selective medium completely inhibits growth of Candida spp. and of Enterococcus spp. and permits reduced growth of selected coliforms and Proteus spp. Growth of Campylobacter ureolyticus on NAV medium is optimal in anaerobic and enriched hydrogen atmospheres. Additionally, an overnight enrichment step using Bolton broth to which 2 g/L sodium formate, 3 g/L sodium fumarate dibasic and the NAV supplement are added, in place of the commercial Bolton broth supplement, allows improved recovery of C. ureolyticus from patients' faeces.

Management of hypotension in preterm infants (The HIP Trial): a randomised controlled trial of hypotension management in extremely low gestational age newborns

BACKGROUND

Extremely preterm babies (delivered at <28 completed weeks of gestation) are frequently diagnosed with hypotension and treated with inotropic and pressor drugs in the immediate postnatal period. Dopamine is the most commonly used first-line drug. Babies who are treated for hypotension more frequently sustain brain injury, have long-term disability or die compared to those who are not. Despite the widespread use of drugs to treat hypotension in such infants, evidence for efficacy is lacking, and the effect of these agents on long-term outcomes is unknown.

HYPOTHESIS

In extremely preterm babies, restricting the use of dopamine when mean blood pressure (BP) values fall below a nominal threshold and using clinical criteria to determine escalation of support ('restricted' approach) will result in improved neonatal and longer-term developmental outcomes. RESEARCH PLAN: In an international multi-centre randomised trial, 830 infants born at <28 weeks of gestation, and within 72 h of birth, will be allocated to 1 of 2 alternative treatment options (dopamine vs. restricted approach) to determine the better strategy for the management of BP, using a conventional threshold to commence treatment. The first co-primary outcome of survival without brain injury will be determined at 36 weeks' postmenstrual age and the second co-primary outcome (survival without neurodevelopmental disability) will be assessed at 2 years of age, corrected for prematurity.

DISCUSSION

It is essential that appropriately designed trials be performed to define the most appropriate management strategies for managing low BP in extremely preterm babies.

Molecular-based mycobacterial identification in a clinical laboratory setting: a comparison of two methods

Many mycobacterial species are pathogenic to humans, with infection occurring worldwide. Infection with Mycobacterium tuberculosis is a well-described global phenomenon, but other mycobacterial species are increasingly shown to be the cause of both pulmonary and extrapulmonary infection and are managed differently from M. tuberculosis infection. Rapid and accurate differentiation of mycobacterial species is, therefore, critical to guide timely and appropriate therapeutic and public health management. This study evaluates two commercially available DNA strip assays, the Genotype Common Mycobacteria (CM) assay (Hain Lifescience, Nehren, Germany) and the Speed-oligo Mycobacteria assay (Vircell, Spain) for their usefulness in a clinical laboratory setting. Both assays were evaluated on 71 clinical mycobacterial isolates, previously identified using Gen-Probe AccuProbe and through a UK mycobacteriology reference laboratory, as well as 29 non-mycobacterial isolates. Concordant results were obtained for 98% of isolates using both assays. The sensitivity was 97% (95% confidence interval [CI]: 93.3-100%) for the CM assay and 98.6% (95% CI: 95.9-100%) for the Speed-oligo assay. Overall, both assays proved to be useful tools for rapid and sensitive mycobacterial species identification, although interpretation of results was easier with the CM assay. Finally, results were available within one day, compared to current identification times which range between seven days and four weeks.

Validation of a norovirus multiplex real-time RT-PCR assay for the detection of norovirus GI and GII from faeces samples

Norovirus is a leading cause of infectious non-bacterial gastroenteritis. The virus is highly contagious and has multiple modes of transmission, presenting a growing challenge to hospital-based healthcare. In this study, a total of 120 stool samples are tested for the presence of norovirus GI and GII by the Roche two-step Lightcycler 2.0 assay incorporating primers and probes produced by TIB Molbiol, and the results are compared with results from the National Virus Reference Laboratory. The Roche/TIB Molbiol assay produced 51 positive results and 69 negative results. Discrepancy analysis was performed for six conflicting results using a second real-time polymerase chain reaction (PCR) assay (Roche/TIB Molbiol) and this confirmed that four of the five discrepant positive results were true positives. A single discrepant negative result generated by the Roche assay remained negative using the second assay. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated to be 98%, 98.6%, 98.0% and 98.6%, respectively. Melting curve analysis was used to differentiate genogroups I and II and this showed that 92% of strains belonged to genogroup II.

An unusual case of Legionellosis

Legionella species is a common cause of community-acquired pneumonia. However disease due to L. pneumophila serogroup 13 is rare and has not previously been reported in Ireland. It may not be detected by routine Legionella antigen and antibody kits. Due to these limitations, early culture should be considered when legionellosis is suspected. The potential therapeutic benefit of quinolones in the management of this disease is also illustrated.

The role of biopsy in the diagnosis of infections of the central nervous system

CNS infections require prompt appropriate therapy, but do not usually require tissue biopsy for diagnosis. We performed a 5 year audit of CNS infections which required brain or spinal biopsy to determine or confirm a diagnosis of CNS infection. Sixteen cases were identified in which clinical, radiological or additional investigations including culture, serology or PCR for the suspected specific infective agents were not diagnostic. 6 (37.5%) were bacterial abscesses presenting as space-occupying intracerebral lesions with a differential diagnosis of neoplasm. There were 3 (18.7%) cases of toxoplasmosis and 2 (12.5%) cases of aspergillosis. There was one case (6.2%) of herpes simplex encephalitis, one cysticercosis and one progressive multifocal leucoencephalopathy, all biopsied as possible neoplasms. There were 2 (12.5%) cases of spinal tuberculosis, one multifocal, mimicking neurofibromatosis. This review highlights the usefulness of targeted biopsy in the rapid diagnosis of CNS infections. It also emphasizes the lack of specificity of 'negative' culture and serology in certain cases, especially in the setting of immune-compromise.

Severe hyperbilirubinaemia and kernicterus: more caution is needed in newborn jaundice surveillance

Since the 1990s, there has been a re-emergence of cases of severe hyperbilirubinaemia and kernicterus. The current UK incidence of bilirubin encephalopathy is 0.9/100,000 with a higher reported incidence in some countries. Three otherwise healthy newborn infants, who presented with severe hyperbilirubinaemia, including one who developed kernicterus, are reported here. Some of the current challenges in newborn jaundice surveillance are highlighted.

Antimicrobial resistance profiling andfla-typing of Irish thermophillicCampylobacterspp. of human and poultry origin

AIMS

To determine the genetic relationship between a random collection of Irish human and poultry Campylobacter isolates and to determine the frequency of antibiotic resistance.

METHODS AND RESULTS

Sixty-six Campylobacter isolates (34 human and 32 poultry) were typed by restriction fragment length polymorphism of flagellin-A (flaA) PCR products (flaA-RFLP) and by sequencing of the short variable region of flaA (flaA-SVR). FlaA-RFLP identified 58 distinct profiles, while flaA-SVR identified 28 different alleles. The highest level of antibiotic resistance was found for ampicillin (48.5%) followed by nalidixic acid (42.2%) and ciprofloxacin (31.8%). In general, poultry isolates displayed a higher incidence of resistance to the antimicrobials tested than the human isolates.

CONCLUSIONS

A high level of genetic diversity existed among the Campylobacter strains confirming the weak clonality of this species. There was no relationship between antimicrobial resistance and specific genotypes determined by flaA typing suggesting that resistance was due to pressures of antimicrobial therapy.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study emphasizes the need for increased surveillance of antimicrobial susceptibility among Campylobacter isolates in Ireland and the implementation of more stringent control policies relating to the use of antimicrobials in the poultry industry.

Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos

In vivo-derived bovine embryos are of higher quality than those derived in vitro. Many of the differences in quality can be related to culture environment-induced changes in mRNA abundance. The aim of this study was to identify a range of mRNA transcripts that are differentially expressed between bovine blastocysts derived from in vitro versus in vivo culture. Microarray (BOTL5) comparison between in vivo- and in vitro-cultured bovine blastocysts identified 384 genes and expressed sequence tags (ESTs) that were differentially expressed; 85% of these were down-regulated in in vitro cultured blastocysts, showing a much reduced overall level of mRNA expression in in vitro- compared with in vivo-cultured blastocysts. Relative expression of 16 out of 23 (70%) differentially expressed genes (according to P value) were verified in new pools of in vivo- and in vitro-cultured blastocysts, using quantitative real-time PCR. Most (10 out of 16) are involved in transcription and translation events, suggesting that the reason why in vitro-derived embryos are of inferior quality compared with in vivo-derived embryos is due to a deficiency of the machinery associated with transcription and translation.

Phenotypic and genotypic anti-microbial resistance profiles of campylobacters from untreated feedlot cattle and their environment

Anti-microbial resistance is an emerging public health issue. Farmed animals may act as reservoirs and potential sources of anti-microbial resistant Campylobacters. The aim of this study was to investigate the anti-microbial resistance profile of cattle and environmental Campylobacter isolates from normal untreated feedlot cattle, the role of the gyrA Thr-86-Ile mutation in ciprofloxacin-resistant Campylobacter jejuni isolates and the involvement of the tripartite CmeABC efflux system for multi-resistant C. jejuni isolates. The phenotypic anti-microbial resistance testing was carried out on 500 Campylobacter isolates (445 cattle isolates and 55 environmental isolates). In general, there was a higher level of anti-microbial resistance for the environmental isolates compared with the animal isolates, 45% of the animal isolates were resistant to one or more of the seven anti-microbials compared with 84% of the environmental isolates. The combined cattle and environmental Campylobacters had 34 (6.8%) isolates resistant to three or more of the seven anti-microbials tested on all isolates and 11 (2.2%) isolates were resistant to the seven anti-microbials. There was a substantial level of ciprofloxacin-resistant Campylobacters in both animal (8.5%) and environmental (21.8%) isolates. The gyrA Thr-86-Ile mutation was only present in five of 22 ciprofloxacin-resistant C. jejuni isolates investigated. No multi-drug-resistant associated mutation was detected in the CmeB or the CmeR regions investigated. In conclusion, our study observed a substantial level of Campylobacter anti-microbial resistance, highlighting the need for an active anti-microbial surveillance program for food animals in Ireland and the importance of the chosen sampling point can have on the findings of such a program.

Effect of culture environment on gene expression and developmental characteristics in IVF-derived embryos

It is generally accepted that mammalian preimplantation embryos are sensitive to their environment and that conditions of culture can affect future growth and developmental potential both pre- and postnatally. Evidence suggests that while culture conditions during bovine in vitro embryo production can impact somewhat on the developmental potential of the early embryo, the intrinsic quality of the oocyte is the key factor determining the proportion of oocytes developing to the blastocyst stage. In addition, evidence suggests that the period of post fertilization embryo culture is the most critical period affecting blastocyst quality assessed in terms of cryotolerance, gene expression pattern and ability to establish a pregnancy. This paper reviews the current literature, with emphasis on the bovine model, demonstrating evidence for an effect of post fertilization culture environment on embryo gene expression and quality.

Workload and short-term outcome of babies weighing 2,500 grams or more at birth admitted to the paediatric unit of the Rotunda Hospital

BACKGROUND

Audit is important in ensuring adequate use of resources and maintaining optimum standards of care. Most of the emphasis in neonatal audit is focused on very low birth weight infants. However, term and near-term infants account for a significant proportion of the workload in neonatal units and warrant regular audit. In addition, audit of these infants may be useful as a marker of the organisation of the perinatal service.

METHODS

A retrospective audit was performed of all infants with birth weights greater than or equal to 2,500 grams admitted to the neonatal department in the first week of life over a two-year period, examining mode of delivery, level of care, duration of stay, diagnosis and short-term outcome.

RESULTS

Eight hundred and seventy infants were admitted greater than or equal to 2,500 grams birth weight, 54% of all neonatal admissions, during the study period. Six hundred and eighty seven of these infants were admitted in the first week of life and were included in the study; this was 5.8% of infants born with a birth weight 2500 grams or more. Infants born by caesarean section were twice as likely to require admission (9.8%) compared with infants born by vaginal delivery (4.5%). The median length of stay was 3 days (3 hours to 45 days). One hundred and six (15.4%) infants required level 1 or level 2 care. One hundred and eleven infants received normal care, only. Most of these infants were admitted for maternal or social reasons. Other common reasons for admission were jaundice, respiratory disease, neonatal abstinence syndrome and congenital abnormality. Forty-one infants required transfer to another hospital, most commonly for surgical or cardiac conditions. Six infants died after admission. However, only one normally formed infant delivered in our hospital died prior to discharge or transfer. One infant was born at home and four infants who had a lethal congenital abnormality are known to have died following transfer.

CONCLUSION

Term and near-term infants account for a significant proportion of neonatal admissions and deserve regular audit. Many admissions are potentially avoidable. Survival for infants weighing 2,500 grams or greater is excellent. Only one normally formed infant died following admission during the study period. The number of "social" admissions of "well" infants highlighted by this study reflects poorly on the services available for well infant whose mothers are unable to care for them for whatever reason. We recommend regular audit of these infants in order to ensure efficient use of neonatal resources and to ensure optimum levels of neonatal intensive care.

Problem-based, peer-facilitated education about antibiotic prescribing

AIMS

To assess the feasibility and acceptability of a problem-based, peer-facilitated educational workshop about antibiotic prescribingfor GPs.

METHOD

PARTICIPANTS

All 39 GPs working in an average sized Local Health Care Co-operative (LHCC) in Glasgow.

INTERVENTION

Prospective collection of information about 10 prescriptions for antibiotics to assess learning needs in relation to antibiotic prescribing. Two and a half hour workshop involving problem-based group work based on the needs assessment and discussions with a consultant microbiologist, prescribing adviser and academic GP.

EVALUATION

Written feedback about the process of the educational intervention immediately after the workshop and outcome feedback collected after four weeks. Telephone interviews with non-participants.

RESULTS

Twenty-four GPs agreed to participate in the study. 19 of these completed the Needs Assessment and 14 of these completed the workshop. The method of learning needs assessment and the educational workshop were highly acceptable. "No time, too busy" was the main reason given for not taking part in the study.

CONCLUSION

Some GPs are unable to participate as fully as they would like in continuing professional learning activities due to competing workload pressures. Further research is required to investigate the necessary type and balance of learning activities and the barriers to engagement to ensure the most effective use of clinician time available for continuing educational activities.

216 IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN BOVINE EMBRYOS CULTURED IN VIVO OR IN VITRO

The post-fertilization culture environment of the bovine embryo is known to influence the quality of the resulting blastocyst, manifested in terms of morphology, cryotolerance, and the relative gene transcript abundance of several candidate genes. This may have consequences for the pregnancy rate following embryo transfer. The objective of the current study was to take a broader approach toward identifying differentially expressed genes in bovine blastocysts derived from either in vivo or in vitro culture. Presumptive zygotes, produced by in vitro maturation and fertilization, were randomly assigned to one of two groups and cultured for 6 days, either in vitro in SOF medium, or in vivo in the ewe oviduct following transfer by mid-ventral laparotomy. Blastocysts were recovered from both systems on Day 7 after insemination, snap frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from 50 blastocysts for each culture group from each of four replicates using the PicoPureTM RNA Isolation Kit (ARCTURUS, Mountain View, CA 94043, USA). The RiboAmpTM RNA Amplification Kit (ARCTURUS) was used to linearly amplify the mRNA fraction of total RNA using double-stranded cDNA as template in a T7 RNA polymerase-catalyzed amplification. Samples from both culture environments were differentially labelled using N-hydroxysuccinimide (NHS)-activated fluorescent Cy3 or Cy5 dyes (Amersham Pharmacia Ltd., Piscataway, NJ, USA) and were hybridized onto a cDNA microarray. Each microarray contained 3888 total spots, with 932 bovine EST clone inserts developed from a normalized bovine total leukocyte (BOTL) cDNA library and an additional 459 amplicons representing additional genes including cytokines, receptors, signal transduction molecules, transcription and growth factors, enzymes, cell cycle regulators, and cellular components. Data were normalized and an expression ratio calculated between the two groups. This was compared to 1 within each of the 4 replicates by Student's t-test. Microarray analysis identified 15 gene transcripts that were differentially expressed P ≤ 0.05) between blastocysts produced in vivo or in vitro. Among these, four genes involved in transcription (nuclear receptor co-repressor 1, zinc finger protein 22, CCR4-NOT transcription complex, DOT1) and two genes involved in intracellular signalling (proteasome 26S subunit non-ATPase 13 and guanine nucleotide binding protein) had a higher mRNA expression level in blastocysts produced in vivo compared to those produced in vitro. In addition, Connexin 43, a gene involved in gap junction formation, was down regulated following in vitro culture which is consistent with our previous studies. Among the genes up-regulated following in vitro culture were WNT2B wingless-type MMTV integration site, CD103 integrin, and tumor necrosis factor superfamily member 8. In conclusion, we have identified previously uncharacterized, differentially expressed genes involved in cell communication, intracellular signalling, and regulation of transcription in bovine blastocysts cultured in vivo or in vitro. This work was supported by Science Foundation Ireland under Grant No. 02/IN1/B78.

Secondary nucleation of the beta-polymorph of L-glutamic acid on the surface of alpha-form crystals

Evidence is presented for the secondary nucleation of beta-L-glutamic acid on the surface of the alpha-polymorph, using a combination of Scanning Electron Microscopy and Raman spectroscopy.

Overexpression of insulin-like growth factor II (IGFII) in ZR-75-1 human breast cancer cells: higher threshold levels of receptor (IGFIR) are required for a proliferative response than for effects on specific gene expression

Previous transfection experiments using a zinc-inducible expression vector have shown that overexpression of insulin-like growth factor II (IGFII) in MCF7 human breast cancer cells can reduce dependence on oestrogen for cell growth in vitro (DALY RJ, HARRIS WH, WANG DY, DARBRE PD. (1991) Cell Growth Differentiation 2, 457-464.). Parallel transfections now performed into another oestrogen-dependent human breast cancer cell line (ZR-75-1) yielded three clones of transfected ZR-75-1 cells that produced levels of zinc-inducible IGFII mRNA and secreted mature IGFII protein similar to those found in the transfected MCF7 cells. However, unlike in MCF7 cells, no resulting effects were found on cell growth in the ZR-75-1 clones, even though the ZR-75-1 clones possessed receptors capable of binding 125I-IGFI and showed a growth response to exogenously added IGFII. Medium conditioned by the ZR-75-1 clones could stimulate growth of untransfected MCF7 cells, indicating that the secreted IGFII protein was bioactive. Furthermore, zinc-induced IGFII was capable of increasing both pS2 mRNA levels and CAT activity from a transiently transfected AP1-CAT gene in the ZR-75-1 clones. Constitutive co-overexpression of the protein processing enzyme PC2 resulted in reduced levels of large forms of zinc-inducible IGFII, but zinc treatment still produced no effect on cell growth rate. Finally, however, constitutive co-overexpression of the type I IGF receptor (IGFIR) did result in zinc-inducible increased basal cell growth and reduced dependence on oestrogen for cell growth. These results demonstrate that while overexpression of IGFII per se was sufficient to deregulate MCF7 cell growth, the ZR-75-1 cells are limited in their proliferative response by their intrinsic receptor levels. However, although the proliferative response was limited, molecular responses (expression of pS2 and AP1-CAT) were not limited, indicating that different cellular responses can have different threshold receptor level requirements.