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Abstract Background Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environments. Compared to its coastal relative Thalassiosira pseudonana, the oceanic diatom Thalassiosira oceanica is highly tolerant to iron limitation. The adaptation to low-iron conditions in T. oceanica has been attributed to a decrease in the photosynthetic components that are rich in iron. Genomic information on T. oceanica may shed light on the genetic basis of the physiological differences between the two species. Results The complete 141790 bp sequence of the T. oceanica chloroplast genome [GenBank: GU323224], assembled from massively parallel pyrosequencing (454) shotgun reads, revealed that the petF gene encoding for ferredoxin, which is localized in the chloroplast genome in T. pseudonana and other diatoms, has been transferred to the nucleus in T. oceanica. The iron-sulfur protein ferredoxin, a key element of the chloroplast electron transport chain, can be replaced by the iron-free flavodoxin under iron-limited growth conditions thereby contributing to a reduction in the cellular iron requirements. From a comparison to the genomic context of the T. pseudonana petF gene, the T. oceanica ortholog can be traced back to its chloroplast origin. The coding potential of the T. oceanica chloroplast genome is comparable to that of T. pseudonana and Phaeodactylum tricornutum, though a novel expressed ORF appears in the genomic region that has been subjected to rearrangements linked to the petF gene transfer event. Conclusions The transfer of the petF from the cp to the nuclear genome in T. oceanica represents a major difference between the two closely related species. The ability of T. oceanica to tolerate iron limitation suggests that the transfer of petF from the chloroplast to the nuclear genome might have contributed to the ecological success of this species.

Feline chronic gingivostomatitis (FCGS) is a debilitating inflammatory oral mucosal disease with a multifactorial etiology. The clinical diagnosis of FCGS is made based on inspection of severe inflammatory lesions and histological confirmation rather than a molecular diagnostic outcome. This gap limits the ability to provide an early diagnosis. In this report, we seek to provide additional diagnostic tools using genomics to aid in providing clinically relevant information. The use of in-depth diagnostic tools, like transcriptomics of diseased tissues, to diagnose FCGS and stratify patients into predictive treatment response groups would dramatically improve both clinical decisions and patient outcomes. In this study, we addressed the gap in diagnostic options using transcriptomic analysis of caudal oral mucosal swab specimens coupled to detailed medical record linkage of FCGS-affected cats undergoing tooth extractions and in some cases administration of mesenchymal stromal cells (MSCs). To better identify markers of disease and potential response to treatment, the transcriptomes of FCGS-afflicted cats were compared to those of healthy cats and those with chronic periodontitis to clearly establish diagnostic biomarker signal transduction connections. Phosphatidylinositol 3-kinase/Ak strain transforming (PI3K/AKT) and stress-activated protein kinases/Jun N-terminal kinase (SAP/JNK) signaling pathways were significantly differentially regulated in FCGS-afflicted cats. Activation of these pathways also differed in the treatment response groups. In conjunction, the enzymes Caspase 4 (CASP4), matrix metalloproteinase-8 (MMP8), and prostaglandin-endoperoxide synthase 2 (PTGS2) were identified as potential biomarkers for the prediction of treatment response outcomes. The observations in the case study support the use of transcriptomics of FCGS patients to contribute to improved molecular diagnostics for the diagnosis and treatment of FCGS.

Background: Biogeochemical elemental cycling is driven by primary production of biomass via phototrophic phytoplankton growth, with 40% of marine productivity being assigned to diatoms. Phytoplankton growth is widely limited by the availability of iron, an essential component of the photosynthetic apparatus. The oceanic diatom Thalassiosira oceanica shows a remarkable tolerance to low-iron conditions and was chosen as a model for deciphering the cellular response upon shortage of this essential micronutrient., Results: The combined efforts in genomics, transcriptomics and proteomics reveal an unexpected metabolic flexibility in response to iron availability for T. oceanica CCMP1005. The complex response comprises cellular retrenchment as well as remodeling of bioenergetic pathways, where the abundance of iron-rich photosynthetic proteins is lowered, whereas iron-rich mitochondrial proteins are preserved. As a consequence of iron deprivation, the photosynthetic machinery undergoes a remodeling to adjust the light energy utilization with the overall decrease in photosynthetic electron transfer complexes., Conclusions: Beneficial adaptations to low-iron environments include strategies to lower the cellular iron requirements and to enhance iron uptake. A novel contribution enhancing iron economy of phototrophic growth is observed with the iron-regulated substitution of three metal-containing fructose-bisphosphate aldolases involved in metabolic conversion of carbohydrates for enzymes that do not contain metals. Further, our data identify candidate components of a high-affinity iron-uptake system, with several of the involved genes and domains originating from duplication events. A high genomic plasticity, as seen from the fraction of genes acquired through horizontal gene transfer, provides the platform for these complex adaptations to a low-iron world.

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeo dactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.

Background and Purpose: In research facilities using non-human primates, crown-height reduction with partial coronal pulpectomy ("vital pulpotomy") is routinely performed on canine teeth of adult male monkeys to reduce self-trauma and the potential for injury to staff or cage-mates. Success of pulpotomy techniques in humans is reportedly 40 to 60%. Failure leads to chronic inflammation and pulp necrosis, which introduces variability in research animals, and may affect research results. The purpose of the study reported here was to determine failure rate of this procedure by evaluating clinical and radiographic findings at 3, 9, and 24 months after crown amputation and partial coronal pulpectomy of maxillary canines in adult male rhesus monkeys., Methods: Forty-seven maxillary canine teeth from 24 adult male rhesus monkeys were treated by use of crown amputation and partial coronal pulpectomy, using standard dental technique. Follow-up clinical and radiographic examination was performed 3, 9, and 24 months after surgery., Results: At three months after surgery, there was no clinical evidence of failure at any of the teeth. On the basis of radiographic findings, 2 of 47 teeth had failed and one was suspicious for early failure. At nine months, clinical evidence of failure was not apparent; radiographically, 5 of 44 teeth appeared to have failed and 3 others were suspect. Two years post-operatively, failure was clinically evident at two teeth, with radiographic evidence of failure in five teeth, and suspicion of early failure in an additional six of 41 teeth [corrected]., Conclusions: The failure rate of crown amputation and partial coronal pulpectomy of canine teeth in adult male rhesus monkeys is high, and the chronic inflammation associated with this is cause for concern.

Objective: To determine patterns of alveolar bone loss (periodontitis) and other lesions evident on full-mouth survey radiographs of cats., Design: Retrospective study., Animals: 147 cats., Procedure: Full-mouth radiographs were evaluated for evidence and severity of alveolar bone loss, odontoclastic resorption lesions (ORL), retained roots, missing teeth, signs of endodontic disease secondary to periodontitis, and apical resorption., Results: 106 (72%) cats had some degree of periodontitis, 100 (68%) were missing teeth, 98 (67%) had ORL, 78 (53%) had expansion of the buccal alveolar bone at 1 or more canine teeth, 75 (51%) had retained roots, 48 (33%) had apical resorption, and 12 (8%) had signs of endodontic disease secondary to periodontitis. Cats < 4 years old were not significantly more likely than the general population to have normal alveolar bone height. Prevalence of ORL increased with age, but cats > or =13 years old were less likely than the general population to have moderate or severe generalized periodontitis. Purebred cats were not significantly more likely to have periodontitis or ORL than mixed-breed cats., Conclusions and Clinical Relevance: Results suggest that periodontitis is common in cats and that horizontal bone loss is the most common radiographic pattern of alveolar bone loss. Purebred cats were not more likely than mixed-breed cats to have ORL or periodontitis, but when they did have periodontitis, it was more likely to be moderate to severe. Cats with ORL were less likely than cats without ORL to have normal alveolar bone height and more likely to have severe focal vertical bone loss.

Objective: To determine whether odontoclastic resorption lesions were associated with radiographic evidence of periapical lucencies in cats., Design: Retrospective study., Animals: 265 feline dental patients., Procedure: Full-mouth radiographs were examined for evidence of odontoclastic resorption lesions, periapical lucencies, periodontitis, and fractured teeth., Results: Odontoclastic resorption lesions affecting 567 teeth were identified in 161 (60.8%) cats. Periapical lucencies were identified in 53 teeth in 35 cats. Periapical lucencies were most commonly associated with fractured teeth (25 teeth with periapical lucencies) and severe periodontitis (21 teeth). None of the periapical lucencies appeared to be specifically associated with resorption lesions. Prevalence of periapical lucencies in cats with resorption lesions was not significantly different from prevalence in cats without., Conclusions and Clinical Relevance: Results suggest that although odontoclastic resorption lesions are common in cats, pulpal involvement associated with these lesions does not appear to be associated with development of radiographically detectable periapical lucencies. Crown amputation with intentional root retention may, therefore, be a suitable alternative to extraction in selected cats with odontoclastic resorption lesions.