Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants

The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.

Transcriptome and DNA methylome divergence of inflorescence development between two ecotypes in Panicum hallii

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the two major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMRs-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits

Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.

Heart in Heart: A Case Report of Giant Left Atrial Appendage Aneurysm

Left atrial appendage aneurysm (LAAA) is a rare cardiac anomaly. The cause mostly due to congenital, but can be acquired also. Patient may remain asymptomatic or may present with variable symptom. It can predispose to hazardous adverse events, including atrial fibrillation, myocardial infarction, cardiac dysfunction and life-threatening systemic thromboembolism. Simple imaging, electrocardiography and echocardiography can diagnose this rare cardiac anomaly. We are reporting a case who presented to us at 5 years of age with palpitation, chest pain and dizziness with arrythmia that developed one month back; he visited our outpatient department of the National Heart Foundation Hospital & Research Institute Hospital, Dhaka, Bangladesh on 13th February 2020. We diagnosed left atrial appendage aneurysm with mitral valve prolapse with atrial arrhythmia thereafter surgical resection of aneurysmal part along with mitral valve annuloplasty done by mid sternotomy and maze therapy. Postoperative period was uneventful and discharged after 6th post operative day.

Natural variation in growth and leaf ion homeostasis in response to salinity stress in Panicum hallii

Soil salinity can negatively impact plants growth, development and fitness. Natural plant populations restricted to coastal environments may evolve in response to saline habitats and therefore provide insights into the process of salinity adaptation. We investigated the growth and physiological responses of coastal and inland populations of Panicum hallii to experimental salinity treatments. Coastal genotypes demonstrated less growth reduction and superior ion homeostasis compared to the inland genotypes in response to saline conditions, supporting a hypothesis of local adaptation. We identified several QTL associated with the plasticity of belowground biomass, leaf sodium and potassium content, and their ratio which underscores the genetic variation present in this species for salinity responses. Genome-wide transcriptome analysis in leaf and root tissue revealed tissue specific overexpression of genes including several cation transporters in the coastal genotype. These transporters mediate sodium ion compartmentalization and potassium ion retention and thus suggests that maintenance of ionic homeostasis of the coastal genotypes might be due to the regulation of these ion transporters. These findings contribute to our understanding of the genetics and molecular mechanisms of salinity adaptation in natural populations, and widens the scope for genetic manipulation of these candidate genes to design plants more resilient to climate change.

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

Geographic patterns of genomic diversity and structure in the C4 grass Panicum hallii across its natural distribution

Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C₄ grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass

Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost-effective 3'-Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C₄ perennial grass, Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine-scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis-regulatory elements and biological processes under short- and long-day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod-dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well-known GI-interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.

Gene Expression analysis associated with salt stress in a reciprocally crossed rice population

The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed Horkuch with high yielding but salt sensitive IR29 to detect the complement of genes that were responsible for conferring salt tolerance versus sensitivity at the seedling developmental stage. We looked at tolerant and sensitive F3 families from individual F2 segregating plants and analyzed them for differential gene expressions using RNAseq. In general, we observed higher numbers of genes differentially expressed in leaves compared to root tissues. This included both upregulation and downregulation of gene expression across our experimental factors. Gene expression decreased in sensitive leaf after stress exposure where tolerant plants showed the opposite trend. In root, tolerant plants expression decreased at higher time points of stress exposure. We also observed a strong maternal cytoplasmic effect on gene expression and this was most evident in roots where there was upregulation in functional enrichments related to phosphorylation, electron carriers, transporter and cation transmembrane activities. Stress groups (tolerant and sensitive) response in F3 families were distinctive in both cytoplasmic backgrounds and involved uniquely upregulated genes in tolerant progenies including membrane sensor proteins, enzymes involved with signaling pathways, such as those producing trehalose and G-protein coupled receptor proteins, photosynthesis-related enzymes and golgi body recycling as well as prolamin precursor proteins involved in refolding of proteins. On the other hand, sensitivity was found to be associated with differential upregulation of only a few redox proteins and higher number of apoptosis related genes compared to the tolerant response. Overall, our highly replicated experimental design was powerful and allowed the detection of relatively subtle differential expression. Our future goal is to correlate these expression differences with QTLs in this population, which would help identify the relative importance of specific genetic loci and provide a direct avenue for combining higher levels of salt tolerance with better agronomic traits in rice.

Abstract P3-10-11: Clinical implications of 63-gene signature associated with response to PARP inhibition in triple-negative and luminal B breast cancer

Background: Two recent randomized phase 3 trials have demonstrated that treatment with PARP inhibitors results in an improvement in progression-free survival (PFS) in metastatic, BRCA-mutant, HER2-negative breast cancer patients. We have previously identified a pathway-enriched 63-gene expression signature predictive of response to olaparib in seven patient-derived xenograft breast tumors, with a high overall accuracy of 86%. We found that the prevalence of our gene signature was 45% in a cohort of triple-negative breast cancer (TNBC) patients. We wanted to better understand if there were correlations between our 63-gene signature and other known prognostic markers and to determine the prognostic significance of our mutational gene signature in different PAM50 breast cancer subtypes.

Methods: We used a publicly available dataset from the NCI GDC Data Portal of TNBC patients (n = 82) to undertake clinico-pathological correlations with our 63-gene expression signature. We correlated the presence or absence of the signature with age, tumor size, lymph node status, and stage using chi2 analysis, in addition to overall survival (OS) and PFS with STATA SE. We also correlated our gene signature with known TNBC subtypes from TNBCtype. Using the METABRIC cohort (n = 2509), we looked at the mutational frequency of our gene set in cBioPortal in different breast cancer subtypes and determined the prognostic value in each subtype.

Results: We did not find any statistically significant correlations between the 63-gene expression signature and age, tumor size, lymph node status, or stage amongst the 82 TNBC patients. All TNBC subtypes including 2 basal-like, immunomodulatory, low androgen receptor, 2 mesenchymal-based, and unspecified were identified in both gene-signature predicted sensitive and resistant groups, but there were no statistically significant differences between groups. The median follow-up of the TNBC cohort was 24 months, and no statistically significant associations were identified with OS or PFS. In the METABRIC cohort, the mutational frequency of any of the 63 genes for the following subgroups was identified: basal (n = 209), 85.2%; HER2+ (n = 224), 68.8%; claudin-low (n = 218), 48.2%; luminal B (n=475), 25.1%; and luminal A (n=700), 12.7%. The median follow-up of the METABRIC cohort was 127 months. We found that patients with a mutation in any of the 63 genes demonstrated a poorer overall survival, 122.8 months, in comparison to patients without any mutation, 164.6 months (P = 0.0002). In particular, luminal B patients with a mutation in any of these genes demonstrated a poorer overall survival, 90.0 months, in comparison to patients without a mutation, 132.1 months (P = 0.009). No statistically significant difference in overall survival was observed for patients with or without any mutation amongst the luminal A subtype (P = 0.26).

Conclusion: We found that patients with a mutation from our 63-gene set demonstrated a worse prognosis in comparison to patients without a mutation amongst the luminal B subtype. This is suggestive that there may be a role for our 63-gene signature to select patients amongst the luminal B subtype who may benefit from PARP inhibition.

Citation Format: Beniey M, Marois F, Haque T, Hassan S. Clinical implications of 63-gene signature associated with response to PARP inhibition in triple-negative and luminal B breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-11.

A Case of Single Atrium, Mitral Valve Prolapse Spontaneously - Closed Inlet VSD with Polydactyly

Single Atrium is a complex cardiac anomaly and generally a component of certain congenital syndromes. It is extremely rare for SA to be observed as an isolated defect. We report here a 14 year-old male patient with SA with MVP with spontaneously-closed inlet-VSD with polydactyly. He was examined first at "L. Harun Health Complex" 77 Sehora, Mymensingh, Bangladesh on 11th September 2016 and then at National Heart Foundation Hospital, Mirpur, Dhaka, Bangladesh on 17th October 2016.

Investigation of a New Microcapsule Membrane Combining Alginate, Chitosan, Polyethylene Glycol and Poly-L-Lysine for Cell Transplantation Applications

Microencapsulation of living cells may serve as an alternative therapy for patients requiring organ transplants. One of the limiting factors in the progress of such therapy is attaining a biocompatible and mechanically stable polymer. The current study investigates the potential of a novel membrane combining alginate, chitosan, polyethylene glycol (PEG) and poly-L-lysine (PLL) with the objective of proposing a membrane suitable for cell entrapment that may overcome some of the shortcomings of the widely studied alginate-poly-L-lysine-alginate (APA) capsules. The novel microcapsule was formulated using a 1.5% alginate solution coated with 0.05% chitosan, 0.1% PEG and 0.05% poly-L-lysine with a final layer of 0.1% alginate. Microcapsules having a diameter of 450 ± 30 μm were prepared. Upon citrate treatment, the membrane remained intact and retained its spherical structure. The membrane was able to support liver cell proliferation and the encapsulated cells were capable of secreting proteins. The study demonstrated that the new membrane can be used for cell entrapment. However, further investigations are needed to assess its potential for long term transplantation and usage in the development of bioartificial organs.

Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice

Global increase in salinity levels has made it imperative to identify novel sources of genetic variation for tolerance traits, especially in rice. The rice landrace Horkuch, endemic to the saline coastal area of Bangladesh, was used in this study as the source of tolerance in reciprocal crosses with the sensitive but high-yielding IR29 variety for discovering transcriptional variation associated with salt tolerance in the resulting populations. The cytoplasmic effect of the Horkuch background in leaves under stress showed functional enrichment for signal transduction, DNA-dependent regulation and transport activities. In roots the enrichment was for cell wall organization and macromolecule biosynthesis. In contrast, the cytoplasmic effect of IR29 showed upregulation of apoptosis and downregulation of phosphorylation across tissues relative to Horkuch. Differential gene expression in leaves of the sensitive population showed downregulation of GO processes like photosynthesis, ATP biosynthesis and ion transport. Roots of the tolerant plants conversely showed upregulation of GO terms like G-protein coupled receptor pathway, membrane potential and cation transport. Furthermore, genes involved in regulating membrane potentials were constitutively expressed only in the roots of tolerant individuals. Overall our work has developed genetic resources and elucidated the likely mechanisms associated with the tolerance response of the Horkuch genotype.

Comparative genomics of two jute species and insight into fibre biogenesis

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production¹. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species² in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Enhanced Salt Tolerance Conferred by the Complete 2.3 kb cDNA of the Rice Vacuolar Na(+)/H(+) Antiporter Gene Compared to 1.9 kb Coding Region with 5' UTR in Transgenic Lines of Rice

Soil salinity is one of the most challenging problems that restricts the normal growth and production of rice worldwide. It has therefore become very important to produce more saline tolerant rice varieties. This study shows constitutive over-expression of the vacuolar Na(+)/H(+) antiporter gene (OsNHX1) from the rice landrace (Pokkali) and attainment of enhanced level of salinity tolerance in transgenic rice plants. It also shows that inclusion of the complete un-translated regions (UTRs) of the alternatively spliced OsNHX1 gene provides a higher level of tolerance to the transgenic rice. Two separate transformation events of the OsNHX1 gene, one with 1.9 kb region containing the 5' UTR with CDS and the other of 2.3 kb, including 5' UTR, CDS, and the 3' UTR regions were performed. The transgenic plants with these two different constructs were advanced to the T3 generation and physiological and molecular screening of homozygous plants was conducted at seedling and reproductive stages under salinity (NaCl) stress. Both transgenic lines were observed to be tolerant compared to WT plants at both physiological stages. However, the transgenic lines containing the CDS with both the 5' and 3' UTR were significantly more tolerant compared to the transgenic lines containing OsNHX1 gene without the 3' UTR. At the seedling stage at 12 dS/m stress, the chlorophyll content was significantly higher (P < 0.05) and the electrolyte leakage significantly lower (P < 0.05) in the order 2.3 kb > 1.9 kb > and WT lines. Yield in g/plant in the best line from the 2.3 kb plants was significantly more (P < 0.01) compared, respectively, to the best 1.9 kb line and WT plants at stress of 6 dS/m. Transformation with the complete transcripts rather than the CDS may therefore provide more durable level of tolerance.

Projections from the dorsal peduncular cortex to the trigeminal subnucleus caudalis (medullary dorsal horn) and other lower brainstem areas in rats

This study has revealed direct projections from the dorsal peduncular cortex (DP) in the medial prefrontal cortex (mPfC) to the trigeminal brainstem sensory nuclear complex and other lower brainstem areas in rats. We first examined the distribution of mPfC neurons projecting directly to the medullary dorsal horn (trigeminal subnucleus caudalis [Vc]) and trigeminal subnucleus oralis (Vo) which are known to receive direct projections from the lateral prefrontal cortex (insular cortex). After injections of the retrograde tracer Fluorogold (FG) into the rostro-dorsomedial part of laminae I/II of Vc (rdm-I/II-Vc), many neurons were labeled bilaterally (with an ipsilateral predominance) in the rostrocaudal middle level of DP (mid-DP) and not in other mPfC areas. After FG injections into the lateral and caudal parts of laminae I/II of Vc, or the Vo, no neurons were labeled in the mPfC. We then examined projections from the mid-DP by using the anterograde tracer biotinylated dextranamine (BDA). After BDA injections into the mid-DP, many axons and terminals were labeled bilaterally (with an ipsilateral predominance) in the rdm-I/II-Vc, periaqueductal gray and solitary tract nucleus, and ipsilaterally in the parabrachial nucleus and trigeminal mesencephalic nucleus. In addition, the connections of the mid-DP with the insular cortex were examined. Many BDA-labeled axons and terminals from the mid-DP were also found ipsilaterally in the caudalmost level of the granular and dysgranular insular cortex (GI/DI). After BDA injections into the caudalmost GI/DI, many axons and terminals were labeled ipsilaterally in the mid-DP. The projections from the mid-DP to the rdm-I/II-Vc and other brainstem nuclei suggest that mid-DP neurons may regulate intraoral and perioral sensory processing (including nociceptive processing) of rdm-I/II-Vc neurons directly or indirectly through the brainstem nuclei. The reciprocal connections between the mid-DP and caudalmost GI/DI suggest that this regulation may involve mid-DP interactions with the caudalmost GI/DI neurons.

Pregnancy outcome in a case of non-obstructive hypertrophic cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is a relatively common genetic disorder (1:500) inherited as an autosomal dominant trait. It is caused by mutations in any one of 10 genes encoding protein components of cardiac sarcomere. Some theoretically calculated risks exist when patients with HCM become pregnant. The physiologic increase of cardiac output and increased stroke volume may be impaired due to the non-compliant ventricular walls. In the first trimester, the physiologic hypervolemia of pregnancy to some extent counteracts the natural decrease in peripheral vascular resistance which would have otherwise provoked an obstruction gradientin systolic flow. As pregnancy advances, the vena caval compression may decrease venous return causing cardiac compromise, whereas the stress of labour may precipitate arrhythmia. We report our experience of a pregnancy with co-existant non-obstructive hypertrophic cardiomyopathy and nodal bradycardia ultimately resulting in pre-term delivery, neonatal death and maternal death in puerperium from overt cardiac failure after a relatively uneventful gestation.

Somatotopic direct projections from orofacial areas of primary somatosensory cortex to pons and medulla, especially to trigeminal sensory nuclear complex, in rats

The primary somatosensory cortex (S1) projects to the thalamus and brainstem somatosensory nuclei and modulates somatosensory information ascending to the S1 itself. However, the projections from the S1 to the brainstem second-order somatosensory neuron pools have not been fully studied. To address this in rats, we first revealed the somatotopic representation of orofacial areas in the S1 by recording cortical surface potentials evoked by stimulation of the lingual, mental, infraorbital, and frontal nerves. We then examined the morphology of descending projections from the electrophysiologically defined orofacial S1 areas to the pons and medulla after injections of an anterograde tracer, biotinylated dextranamine (BDA), into the orofacial S1 areas. BDA-labeled axon terminals were seen mostly in the trigeminal sensory nuclear complex (TSNC) and had a strong contralateral predominance. They also showed a somatotopic arrangement in dorsoventral and superficial-deep directions within almost all rostrocaudal TSNC levels, and in a rostrocaudal direction within the trigeminal caudal subnucleus. In the principal nucleus (Vp) or oral subnucleus (Vo) of TSNC, the BDA-labeled axon terminals showed a somatotopic arrangement closely matched to that of the electrophysiologically defined projection sites of orofacial primary afferents; these projection sites were marked by injections of a retrograde tracer, Fluorogold (FG), into the Vp or Vo. The FG injections labeled a large number of S1 neurons, with a strong contralateral predominance, in a somatotopic manner, which corresponded to that presented in the electrophysiologically defined orofacial S1 areas. The present results suggest that the orofacial S1 projections to somatotopically matched regions of trigeminal second-order somatosensory neuron pools may allow the orofacial S1 to accurately modulate orofacial somatosensory transmission to higher brain centers including the orofacial S1 itself.

Investigation on Abrasive Free Copper Chemical Mechanical Planarization for Cu/low k and Cu/ultra low k interconnects

Abrasive Free Copper Chemical Mechanical Polishing (AF-CMP) was developed for Cu/low k materials. Blanket film Cu removal rate of 6000 Å/min with very less non-uniformity of 3% achieved for polishing pressure of 1.5 psi. CMP process window and lower critical pressure were identified with pattern wafers. Material removal mechanism was studied using surface morphology of Copper blanket wafers polished using different pressure, rotation rate and slurry flow rate. Material Removal Mechanism (wear mechanism) such as Chemical wear (etching) and mechanical wear (fatigue wear, particle adhesion wear and abrasion wear) have been found. The increase of slurry flow rate and relative velocity and the decrease of pressure give the dominance of chemical wear in material removal mechanism, and vice versa. Dishing control was achieved during Cu polish using different carrier/platen speed for Cu/SiLKTM patterned wafers. The cumulative distribution of the metal line-to-line leakage current measurements of wafers shows good performance and it is comparable to abrasive process.

Fulminant hepatitis following primary herpes simplex virus infection

Fulminant hepatic failure (FHF) is a rare but well-recognized complication of primary herpes simplex virus (HSV) infection in immunocompromised patients. Here, we report two cases of acute hepatitis and FHF secondary to primary HSV type 1 infection following renal transplantation in the absence of any mucocutaneous manifestation. High levels of HSV type-1 DNA were detected in the blood. Both patients were seronegative for HSV 1 and HSV 2 immunoglobulin G (IgG) before transplantation, whereas the donor of patient 1 was HSV 1 IgG-positive but had no viremia and the donor of patient 2 was HSV-seronegative. Patient 1 recovered with acyclovir and immunoglobulin whereas patient 2 did not respond and succumbed to death. HSV-seronegative patients are potentially at risk of developing severe primary HSV disease following transplantation, particularly in the absence of routine anti-viral prophylaxis. HSV infection should always be excluded in transplant patients with hepatic dysfunction.

Corticofugal direct projections to primary afferent neurons in the trigeminal mesencephalic nucleus of rats

Little is known about projections from the cerebral cortex to the trigeminal mesencephalic nucleus (Vmes) which contains the cell bodies of primary sensory afferents innervating masticatory muscle spindles and periodontal ligaments of the teeth. To address this issue, we employed retrograde (Fluorogold, FG) and anterograde (biotinylated dextranamine, BDA) tracing techniques in the rat. After injections of FG into the Vmes, a large number of neurons were retrogradely labeled in the prefrontal cortex including the medial agranular cortex, anterior cingulate cortex, prelimbic cortex, infralimbic cortex, deep peduncular cortex and insular cortex; the labeling was bilateral, but with an ipsilateral predominance to the injection site. Almost no FG-labeled neurons were found in the somatic sensorimotor cortex. After BDA injections into the prefrontal cortex, anterogradely labeled axon fibers and boutons were distributed bilaterally in a topographic pattern within the Vmes, but with an ipsilateral predominance to the injection site. The rostral Vmes received more preferential projections from the medial agranular cortex, while the deep peduncular cortex and insular cortex projected more preferentially to the caudal Vmes. Several BDA-labeled axonal boutons made close associations (possible synaptic contacts) with the cell bodies of Vmes neurons. The present results have revealed the direct projections from the prefrontal cortex to the primary sensory neurons in the Vmes and their unique features, suggesting that deep sensory inputs conveyed by the Vmes neurons from masticatory muscle spindles and periodontal ligaments are regulated with specific biological significance in terms of the descending control by the cerebral cortex.

Tumour necrosis factor gene polymorphism: a predictive factor for the development of post-transplant lymphoproliferative disease

Background:

Epstein–Barr virus-positive post-transplant lymphoproliferative disease (PTLD) is a potentially lethal complication of iatrogenic immunosupression after transplantation. Predicting the development of PTLD allowing early and effective intervention is therefore of importance. Polymorphisms within cytokine genes are implicated in susceptibility to, and progression of, disease however the published data are often conflicting. We undertook investigation of polymorphic alleles within cytokine genes in PTLD and non-PTLD transplant cohorts to determine risk factors for disease.

Methods:

SSP-PCR was used to analyse single nucleotide polymorphism within tumour necrosis factor (TNF)-α, interleukin- 1, -6, -10 and lymphotoxin-α genes. The TNF-α levels were measured by standard enzyme-linked immuno-absorbant assay.

Results:

We show an association between variant alleles within the TNF-α promoter (−1031C (P=0.005)); −863A (P=0.0001) and TNF receptor I promoter regions (−201T (P=0.02)); −1135C (P=0.03) with the development of PTLD. We also show an association with TNF-α promoter haplotypes with haplotype-3 significantly increased (P=0.0001) and haplotype-1 decreased (P=0.02) in PTLD patients compared to transplant controls. Furthermore, we show a significant increase (P=0.02) in the level of TNF-α in PTLD patient plasma (range 0–97.97 pg ml⁻¹) compared to transplant controls (0–8.147 pg ml⁻¹), with the highest levels found in individuals carrying the variant alleles.

Conclusion:

We suggest that genetic variation within TNF-α loci and the level of plasma cytokine could be used as a predictive risk factor for the development of PTLD.

A review of FGF18: Its expression, signaling pathways and possible functions during embryogenesis and post-natal development

FGF18 is a novel growth factor first reported in 1998. Current evidence suggests that FGF18 may play a prominent role in chondrogenesis and osteogenesis during skeletal development and growth. However, its function extends to many other biological processes. Although there remains much to be discovered and investigated on the functions and mechanisms of FGF18, it may play a role as a useful therapeutic target for various applications. The following review summarizes the current knowledge on FGF18 with special emphasis on its skeletal functions and highlights its potential areas for future research.

An immunohistochemical analysis of the temporal and spatial expression of growth factors FGF 1, 2 and 18, IGF 1 and 2, and TGFbeta1 during distraction osteogenesis

Distraction osteogenesis (DO) is a well established surgical technique that generates new bone by gradual distraction of two bony segments. In this study, we investigated the temporal and spatial profile of FGF 1, 2 and 18, IGF 1 and 2, and TGFbeta1 during distraction osteogenesis using immunohistochemistry. An osteotomy was performed on the right tibia of 13 white male New Zealand rabbits. After a delay of 7 days, distraction was started at a rate of 0.25 mm/12 hrs for 3 weeks which was followed by a 3 week period of consolidation. Immunohistochemical analysis was performed on a weekly interval to determine the expression of the growth factors. Staining of all growth factors was apparent at various levels in the centre and callus region in fibroblasts and chondrocyte cells. FGF2 however, showed continued high expression in osteoblasts. Within two weeks after the end of distraction all growth factors showed a reduction in expression except for FGF18 which maintained high levels of expression (up to 100% staining) throughout the distraction and consolidation phases. The study suggests that in comparison to the other investigated growth factors, FGF18 may play in important role throughout the entire process of distraction osteogenesis.

In-vitro analysis of APA microcapsules for oral delivery of live bacterial cells

Oral administration of microcapsules containing live bacterial cells has potential as an alternative therapy for several diseases. This article evaluates the suitability of the alginate-poly-L-lysine-alginate (APA) microcapsules for oral delivery of live bacterial cells, in-vitro, using a dynamic simulated human gastro-intestinal (GI) model. Results showed that the APA microcapsules were morphologically stable in the simulated stomach conditions, but did not retain their structural integrity after a 3-day exposure in simulated human GI media. The microbial populations of the tested bacterial cells and the activities of the tested enzymes in the simulated human GI suspension were not substantially altered by the presence of the APA microcapsules, suggesting that there were no significant adverse effects of oral administration of the APA microcapsules on the flora of the human gastrointestinal tract. When the APA microcapsules containing Lactobacillus plantarum 80 (LP80) were challenged in the simulated gastric medium (pH = 2.0), 80.0% of the encapsulated cells remained viable after a 5-min incubation; however, the viability decreased considerably (8.3%) after 15 min and dropped to 2.6% after 30 min and lower than 0.2% after 60 min, indicating the limitations of the currently obtainable APA membrane for oral delivery of live bacteria. Further in-vivo studies are required before conclusions can be made concerning the inadequacy of APA microcapsules for oral delivery of live bacterial cells.

Complete regression of posttransplant lymphoproliferative disease using partially HLA-matched Epstein Barr virus-specific cytotoxic T cells

BACKGROUND

Adoptive immunotherapy with autologous and donor-derived cytotoxic T lymphocytes (CTL) has recently been used to treat Epstein Barr virus (EBV)-positive posttransplant lymphoproliferative disease (PTLD).

METHODS AND RESULTS

We report complete regression of EBV-positive PTLD in an 18-month-old small bowel and liver transplant recipient after one infusion of partially human leukocyte antigen (HLA)-matched EBV-specific CTL grown ex vivo from an EBV seropositive unrelated blood donor. No infusion-related toxicity or evidence of graft-versus-host disease was observed. The tumor showed signs of regression within 1 week and EBV load in peripheral blood dropped to undetectable levels. Limiting dilution analyses (LDA) detected no EBV-specific CTL precursor (CTLp) cells before the infusion, and high numbers of CTLp at 4 hr and 24 hr post-CTL infusion. There was a reversal of the CD4/8 ratio in peripheral blood and an increase in HLA-DR positive CD8 cells. The patient has been in complete remission for 24 months.

CONCLUSION

If this success is repeated in more PTLD patients, then stored CTL could be used for antiviral and antitumor therapies in immunocompromised patients.

Visual loss in pregnancy

A 36-year-old preeclamptic woman presented with bilateral visual loss upon recovery from anesthesia following cesarean section. Visual acuity was hand motion OU. Pupillary responses to light were normal, without a relative afferent pupillary defect. Treatment consisted of control of blood pressure and the patient's vision improved to 20/25 OU within 3 days.

Selective inhibition of bacterial dihydroorotate dehydrogenases by thiadiazolidinediones

Dihydroorotate dehydrogenase is a critical enzyme of de novo pyrimidine biosynthesis in prokaryotic and eukaryotic cells. Differences in the primary structure of the enzymes from Gram-positive and -negative bacteria and from mammals indicate significant structural divergence among these enzymes. We have identified a class of small molecules, the thiadiazolidinediones, that inhibit prototypical enzymes from Gram-positive and -negative bacteria, but are inactive against the human enzyme. The most potent compound in our collection functioned as a time-dependent irreversible inactivator of the bacterial enzymes with k(inact)/K(i) values of 48 and 500 M(-1) sec(-1) for the enzymes from Escherichia coli and Enterococcus faecalis, respectively. The data presented here indicate that it is possible to inhibit prokaryotic dihydroorotate dehydrogenases selectively while sparing the mammalian enzyme. Thus, this enzyme may represent a valuable target for the development of novel antibiotic compounds.

Myocardial viability detected by dobutamine echocardiography in patients with chronic coronary artery disease, and long-term outcome after coronary angioplasty

Viable but dysfunctional myocardium detected by dobutamine echocardiography (DE) predicts early improvement in regional left ventricular (LV) function after percutaneous transluminal coronary angioplasty (PTCA). Whether DE can predict the long-term (>2 years) outcome after PTCA is still unclear. Thus, 50 patients (age 60.4+/-9.5 years) with chronic coronary artery disease and regional LV dysfunction who underwent DE 1 week before PTCA to assess myocardial viability were followed for 4.0+/-0.8 years. Regional LV function and LV ejection fraction (LVEF) were evaluated by 2-dimensional echocardiography in patients who remained event-free (cardiac death or myocardial infarction or unstable angina pectoris) after PTCA. At late follow-up (>2 years after PTCA), 29 patients showed regional LV function improvement, 15 showed no improvement, 3 showed worsening and 3 patients had cardiac events (1 nonfatal myocardial infarction and 2 unstable angina pectoris). LVEF improved (0.53+/-0.09 to 0.60+/-0.09, p<0.001) in patients with improved regional LV function, but deteriorated (0.38+/-0.03 to 0.30+/-0.03) in the 3 patients with worsened regional LV function. Of the 29 patients with improvement, 27 (93%) had viable myocardium, whereas only 3 (20%) of the 15 with no improvement had viable myocardium and all 6 of those with poor outcomes (3 with cardiac events and 3 with worsening) had viable myocardium (chi2 = 28.9, p<0.001). Patients with viable myocardium and a poor outcome had a lower mean LVEF before PTCA, and at 1 week and 3 months after PTCA (p = 0.004, <0.001, and =0.001, respectively), and a higher restenosis rate (p = 0.007) than patients with viable myocardium and without a poor outcome. It is concluded that viable myocardium detected by DE may predict long-term improvement in regional and global LV function after PTCA. However, patients with viable myocardium and persistent low LVEF are at risk for cardiac events or worsening of LV function.

Epstein-Barr virus (EBV) associated B-cell lymphoproliferative disease following HLA identical sibling marrow transplantation for aplastic anaemia in a patient with an EBV seronegative donor

BACKGROUND

B-cell lymphoproliferative disorders (BLPD*) caused by Epstein-Barr virus (EBV) occurring after allogeneic bone marrow transplantation (BMT) are usually of donor origin. Treatment such as discontinuation of immunosuppression may be successful in some cases, but infusion of donor T cells results in successful eradication of EBV BLPD in most cases.

METHODS AND RESULTS

We report a case of EBV positive aggressive BLPD after HLA matched sibling BMT for aplastic anaemia. The tumour completely regressed after withdrawal of cyclosporin and donor lymphocyte infusion. However, although the tumor was of donor origin, the donor serum was negative for antibodies to EBV antigens and no EBV-specific cytotoxicity was detected in donor peripheral blood mononuclear cells. The recipient was seropositive for EBV before BMT.

CONCLUSIONS

We speculate that a 'second primary' EBV infection occurred involving donor cells in the recipient during BMT immunosuppression, with subsequent outgrowth of donor-derived BLPD. EBV infection may have been by an endogenous EBV isolate, from external sources, or from third party transfusions.

Non-correlation of in vivo and in vitro parameters of Epstein-Barr virus persistence suggests heterogeneity of B cell infection

Following primary infection Epstein-Barr virus (EBV) establishes a persistent infection which is maintained for the life-time of the host. EBV can be found in a small number of circulating B cells, but the nature of the virus-cell interaction has not been fully established. Several assay systems are used to quantify persistent EBV infection, including PCR amplification of EBV DNA and spontaneous outgrowth of lymphoblastoid cell lines in culture. More recently, outgrowth of EBV-positive B cell tumours in severe combined immunodeficient (SCID) mice inoculated with peripheral blood mononuclear cells (PBMC) from normal EBV-seropositive donors has also been used to study B cell infection in vivo. In the present study we have compared the results of these two biological assay systems with PCR detection of EBV DNA and a regression assay as a measure of host T cell immunity to EBV. PBMC from ten normal EBV-seropositive donors were studied and although each test gave consistent results on repeat assays, no correlation was found between any of the assays tested. This result suggests that each assay measures a separate aspect of EBV persistence in B cells, and indicates a previously unrecognized degree of heterogeneity in the B cell population in which EBV resides.

Reconstitution of EBV-specific T cell immunity in solid organ transplant recipients

EBV-specific autologous CTL were grown in vitro from three adults (two liver transplant recipients and one patient on hemodialysis awaiting kidney retransplant). All CTL lines were TCR alphabeta, CD8 positive cells, EBV specific, and MHC class I restricted. The CTL lines were expanded in vitro and infused in three escalating doses (5 x 10(7), 1 x 10(8), and 2 x 10(8) at monthly intervals. Weekly blood samples were collected following each infusion. EBV-specific CTL precursor cells in peripheral blood were quantitated by limiting dilution analysis, and their effect on EBV load in vivo was assessed by semiquantitative PCR. In all three patients, the numbers of CTL precursor cells increased during the weeks following the infusions and were highest after the third infusion. This level gradually declined but remained above the preinfusion levels for up to 3 mo. EBV genome copy number, on the other hand, dropped following the first infusion and became undetectable thereafter. The EBV DNA level remained lower than the pretransplant level in all patients for up to 3 mo after the last infusion. Our study shows that it is feasible to generate and expand EBV-specific CTL from pretransplant blood samples of solid organ transplant recipients, that these CTL can be stored and infused posttransplant, and that they remain cytotoxic and EBV specific in vivo. The aim of this study is to use these CTL for prevention and treatment of lymphoproliferative disease in solid organ transplant recipients.

Echocardiography and fatty acid single photon emission tomography in predicting reversibility of regional left ventricular dysfunction after coronary angioplasty

AIMS

The present study was performed to evaluate whether echocardiographic assessment of end-diastolic wall thickness and myocardial fatty acid metabolic single-photon emission tomographic imaging with 123I-beta-methyl-iodophenyl pentadecanoic acid could be used to predict the reversibility of dysfunctional left ventricular segments after coronary artery revascularization.

METHODS AND RESULTS

Twenty-eight patients with wall motion abnormalities related to stenosed coronary arteries underwent resting two-dimensional echocardiography and 123I-beta-methyl-iodophenyl pentadecanoic acid single photon emission tomography before coronary angioplasty. A dysfunctional segment was considered viable by the presence of either preserved wall thickness (> or = 75% of the thickness of a normal segment) or preserved fatty acid uptake (> or = 50% of that in normal region). Echocardiography was repeated after successful angioplasty. Functional recovery was observed in 32 (74%) of 43 hypokinetic and nine (100%) of nine akinetic segments with preserved wall thickness and in 11 (79%) of 14 thinned akinetic segments with preserved fatty acid uptake. In contrast, no functional recovery was observed in any of the 13 thinned segments with < 50% fatty acid uptake (eight akinetic and five dyskinetic). Using combined evaluation of both methods, positive and negative predictive values for post-revascularization functional outcome were 79% and 100%, respectively, in all dysfunctional segments; and 87% and 100%, respectively, in akinetic/dyskinetic segments.

CONCLUSIONS

The present study showed that echocardiographic findings of preserved wall thickness and single-photon emission tomography evaluated preserved fatty acid uptake in thinned segments are reliable predictors of post-revascularization functional recovery and the concordant absence of both accurately predict negative outcome.

PCR amplification is more sensitive than tissue culture methods for Epstein-Barr virus detection in clinical material

In this study we have compared the use of PCR and conventional tissue culture methods to detect Epstein-Barr virus (EBV) in peripheral blood mononuclear cells and throat wash samples. The study population included 29 healthy adult and 20 immunocompromised EBV-seropositive donors. The results show significantly higher EBV detection rates by PCR than the tissue culture methods in throat wash samples from both donor groups (P < 0.01 in healthy donors and P < 0.009 in the immunocompromised donors) and in peripheral blood from the immunocompromised but not from the healthy donors (P < 0.008). Furthermore, when EBV DNA detection rates in throat wash cell pellet and supernatant fluid were compared, a higher positive result was obtained with the cell pellets which reached statistical significance in the immunocompromised group (P < 0.02). No correlation was found between positivity in throat wash and peripheral blood from the same donors.

A prospective study in heart and lung transplant recipients correlating persistent Epstein-Barr virus infection with clinical events

BACKGROUND

A 2-year prospective study was set up with 30 cardiothoracic transplant recipients to study Epstein-Barr virus (EBV) infection and immunity and their correlation with clinical events.

METHODS

Regression assays were used to measure EBV-specific cytotoxic T lymphocyte (CTL) function. Tissue culture, immunoblotting, and polymerase chain reaction were used for EBV detection and isolate variation studies.

RESULTS

CTL activity was significantly lower in pretransplant seropositive patients than in healthy controls (P<0.001). CTL response was undetectable in all patients during the first 6 months after transplantation, but returned at levels significantly lower than pretransplant and control levels during the second posttransplant year (P<0.001). Return of CTL function was directly correlated with time of last treated rejection episode (P<0.003) and duration of high plasma levels of cyclosporine (over 400 ng/ml; P<0.003). Significantly higher levels of EBV were detected in peripheral blood during the first 6 months than in pretransplant or control samples (P<0.05). Excretion of EBV in throat washings was significantly lower during the first 3 months when all patients were receiving acyclovir than in pretransplant and control samples (P=0.02). An increase in virus shedding was noted 3-6 months after transplantation, which was significantly higher than in pretransplant patients and controls (P<0.05). Comparison of recipients' and donors' virus isolates in 11 cases showed that seropositive recipients retained their original EBV isolate and did not acquire the donor virus.

CONCLUSIONS

Immunosuppression decreased EBV-specific host immune function, which in turn favored increased EBV load in peripheral blood and increased excretion in the oropharynx. The transfer of donor virus to the seropositive recipients was not observed.