Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

Feeding metabolism in an Indian major carp (Catla catla Lin.) fed on different protein diets

Feeding metabolism in an Indian major carp, Catla catla fingerlings of 10.8+0.56g was investigated in a flow-through water recirculating system. The metabolic energy loss in resting metabolism and feeding metabolism were determined by the indirect method of oxygen consumption followed by multiplication by suitable oxycalorific coefficient. This was done in four metabolic chambers of a respirometer system. Ten fish fingerlings of mean total weight of 109.5, 110.4 and 112.8g/chambers respectively each in two experimental runs of three treatments a, b and c were used. The mean resting metabolic rate during unfed condition showed no significant variation in different treatments. The fish in three treatments a, b and c fed on diets containing 28, 33 and 38% crude protein had significantly different (p<0.05) post-fed SDA magnitude of 497.7, 638.7 and 735.5 mgO2/chamber/day having an equivalent energy loss of 12.68, 14.68 and 15.86 KJ respectively. The SDA co-efficient in three treatments a, b and c were 14.95, 19.00 and 22.36% respectively whereas, respiratory energy - 'R' as % of mean total ingested energy in three treatments were 26.93, 31.17 and 34.74% respectively showing a significant increase (p<0.05) with increase of protein. Feeding metabolism in an Indian major carp (Catla catla Lin.) fed on different protein diets.

Combined effects of polyfluorinated and perfluorinated compounds on primary cultured hepatocytes from rare minnow (Gobiocypris rarus) using toxicogenomic analysis

Polyfluorinated and perfluorinated compounds (PFCs) are used in numerous commercial products and have been ubiquitously detected in the environment as well as in the blood of humans and wildlife. To assess the combined effects caused by PFCs in mixtures, gene expression profiles were generated using a custom cDNA microarray to detect changes in primary cultured hepatocytes of rare minnows exposed to six individual PFCs (perfluorooctanoic acid, perfluorononanoic acid, perfluorodecanoic acid, perfluorododecanoic acid, perfluorooctane sulfonate, and 8:2 fluorotelomer alcohol) and four formulations of the PFCs mixtures. Mixtures as well as individual compounds consistently regulated a particular gene set, which suggests that these conserved genes may play a central role in the toxicity mediated by PFCs. Specifically, a number of genes regulated by the mixtures were identified in this study, which were not affected by exposure to any single component. These genes are implicated in multiple biological functions and processes, including fatty acid metabolism and transport, xenobiotic metabolism, immune responses, and oxidative stress. More than 80% of the altered genes in the PFOA- and PFOS-dominant mixture groups were of the same gene set, while the gene expression profiles from single PFOA and PFOS exposures were not as similar. This work contributes to the development of toxicogenomic approaches in combined toxicity assessment and allows for comprehensive insights into the combined action of PFCs mixtures in multiple environmental matrices. (C) 2009 Elsevier B.V. All rights reserved.

Microcalorimetric investigation of the toxic action of Cr(VI) on the metabolism of Tetrahymena thermophila BF5 during growth

Tetrahymena thermophila BF5 produce heat by metabolism and movement. Using a TAM air isothermal microcalorimeter, the power-time curves of the metabolism of T thermophila BF5 during growth were obtained and the action on them by the addition of Cr(VI) were studied. The morphological change with Cr(VI) coexisted and biomass change during the process of T thermophila BF5 growth were studied by light microscope. Chromium has been regarded as an essential trace element for life. However, hexavalent chromium is a known carcinogen, mutagen, cytotoxicant and strong oxidizing agent. Cr(VI) of different concentration have different effects on T thermophila BF5 growth with the phenomenon of low dose stimulation (0-3 x 10(-5) mol L-1) and high dose inhibition (3 x 10(-5) to 2.4 x 10(-4) mol L-1). The relationship between the growth rate constant (k) and c is a typical U-shaped curve, which is a characteristic of hormesis. T thermophila BF5 cannot grow at all when the concentration of Cr(VI) is up to 2.4 x 10(-4) mol L-1. The microscopic observations agree well with the results obtained by means of microcalorimetry. And T thermophila BF5 had obviously morphological changes by the addition of Cr(VI). (c) 2006 Elsevier B.V. All rights reserved.

Photosynthetic physiology and growth as a function of colony size in the cyanobacterium Nostoc sphaeroides

Algal size can affect the rate of metabolism and of growth. Different sized colonies of Nostoc sphaeroides were used with the aim of determining the effects of colony size on photosynthetic physiology and growth. Small colonies showed higher maximum photosynthetic rates per unit chlorophyll, higher light saturation point, and higher photosynthetic efficiency (a) than large colonies. Furthermore, small colonies had a higher affinity for DIC and higher DIC-saturated photosynthetic rates. In addition, small colonies showed higher photosynthetic rates from 5-45degreesC than large colonies. There was a greater decrease in Fv/Fm after exposure to high irradiance and less recovery in darkness for large colonies than for small colonies. Relative growth rate decreased with increasing colony size. Small colonies had less chl a and mass per unit surface area. The results indicate that small colonies can harvest light and acquire DIC more efficiently and have higher maximum photosynthetic rates and growth rates than large colonies.

Effect of ration and body size on the energy budget of juvenile white sturgeon

Growth and energy budget were measured for three sizes(2.4, 11.1 and 22.5 g) of juvenile white sturgeon Acipenser transmontanus held at 18.5 degrees C and fed tubificid worms at different levels ranging from starvation to ad libitum. For each size-class, specific growth rate increased linearly with increasing ration, and conversion efficiency was highest at the maximum ration. Growth rate decreased with increasing fish size at the maximum ration, but increased with size al each restricted ration. Conversion efficiency increased with increasing ration for each size-class and was usually highest at the maximum ration. Faecal production accounted for 3.2-5.2% of food energy. The proportion of food energy lost in nitrogenous excretion decreased with increasing ration. With increases in ration, the allocation of metabolizable energy to metabolism decreased, while that to growth increased. Fish size had no significant effect on the allocation of metabolizable energy to metabolism or growth. Al the maximum ration, on average 64.9% of metabolizable energy was spent on metabolism, and 35.1% on growth. (C) 1996 The Fisheries Society of the British Isles

EFFECT OF RATION SIZE ON THE GROWTH AND ENERGY BUDGET OF THE GRASS CARP, CTENOPHARYNGODON-IDELLA VAL

Young grass carp (12-13 g) were kept at five ration levels ranging from starvation to ad libitum feeding at 30-degrees-C. They were fed duckweed. Food consumption, absorption efficiency and growth were determined directly, and metabolism and nitrogenous excretion calculated indirectly from energy and nitrogen budgets, respectively. The relationship between specific growth rate and ration size was linear. Absorption efficiency for energy was not affected by ration size and averaged 50.6 +/- 0.57% (mean +/- s.e.). Depending on ration size, energy lost in excretion accounted for 4.5-5.9% of the food energy, energy channelled to metabolism accounted for 34.4-48.3% of the food energy, and energy retained as growth accounted for 6.7-11.9% of the food energy. Regardless of ration, a constant proportion of food energy (30.7%) was accounted for by feeding metabolism (total metabolism minus fasting metabolism). The energy budget at the maximum ration was: 100 C = 49.1F + 4.5U + 3.6R(fa) + 30.9R(fe) + 11.9G, where C, F, U, R(fa), R(fe) and G represent food consumption, faecal production, excretion, fasting metabolism, feeding metabolism and growth, respectively.

Towards manipulation of post-biosynthetic events in secondary metabolism of plant cell cultures

Plant cell cultures have been suggested as a feasible technology for the production of a myriad of plant-derived metabolites. However, commercial application of plant cell culture has met limited success with only a handful of metabolites produced at the pilot- and commercial-scales. To improve the production of secondary metabolites in plant cell cultures, efforts have been devoted predominantly to the optimization of biosynthetic pathways by both process and genetic engineering approaches. Given that secondary metabolism includes-the synthesis. metabolism and catabolism of endogenous compounds by the specialized proteins, this review intends to draw attention to the manipulation and optimization of post-biosynthetic events that follow the formation of core metabolite structures in biosynthetic pathways. These post-biosynthetic events-the chemical and enzymatic modifications, transport, storage/secretion and catabolism/degradation have been largely unexplored in the past. Potential areas are identified where further research is needed to answer fundamental questions that have implications for advanced bioprocess design. Anthocyanin production by plant cell cultures is used as a case study for this discussion, as it presents a good example of compounds for which there are extensive research publications but still no commercial bioprocess. It is perceived that research on post-biosynthetic processes may lead to future opportunities for significant advances in commercial plant cell cultures. (C) 2002 Elsevier Science Inc. All rights reserved.

Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta)

Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790-DN608469, EG016226-EG018540).

Molecular cloning and stress-dependent expression of a gene encoding Delta(12)-fatty acid desaturase in the Antarctic microalga Chlorella vulgaris NJ-7

The psychrotrophic Antarctic alga, Chlorella vulgaris NJ-7, grows under an extreme environment of low temperature and high salinity. In an effort to better understand the correlation between fatty acid metabolism and acclimation to Antarctic environment, we analyzed its fatty acid compositions. An extremely high amount of Delta(12) unsaturated fatty acids was identified which prompted us to speculate about the involvement of Delta(12) fatty acid desaturase in the process of acclimation. A full-length cDNA sequence, designated CvFAD2, was isolated from C. vulgaris NJ-7 via reverse transcription polymerase chain reaction (RT-PCR) and RACE methods. Sequence alignment and phylogenetic analysis showed that the gene was homologous to known microsomal Delta(12)-FADs with the conserved histidine motifs. Heterologous expression in yeast was used to confirm the regioselectivity and the function of CvFAD2. Linoleic acid (18:2), normally not present in wild-type yeast cells, was detected in transformants of CvFAD2. The induction of CvFAD2 at an mRNA level under cold stress and high salinity is detected by real-time PCR. The results showed that both temperature and salinity motivated the upregulation of CvFAD2 expression. The accumulation of CvFAD2 increased 2.2-fold at 15A degrees C and 3.9-fold at 4A degrees C compared to the alga at 25A degrees C. Meanwhile a 1.7- and 8.5-fold increase at 3 and 6% NaCl was detected. These data suggest that CvFAD2 is the enzyme responsible for the Delta(12) fatty acids desaturation involved in the adaption to cold and high salinity for Antarctic C. vugaris NJ-7.

Inhibitory effects and mechanisms of high molecular-weight phlorotannins from Sargassum thunbergii on ADP-induced platelet aggregation

We evaluated the effects of high molecular-weight phlorotannins from Sargassum thunbergii (STP) on ADP-induced platelet aggregation and arachidonic acid (AA) metabolism in New Zealand white rabbits and Wistar rats. The inhibition of STP on platelet aggregation was investigated using a turbidimetric method, and the levels of the terminal products of AA metabolism were measured using the corresponding kits for maleic dialdehyde (MDA), thromboxane B-2 (TXB2) and 6-keto-prostaglandin F-1 alpha (6-keto-PGF(1 alpha)) by colorimetry and radioimmunoassay, as appropriate. We found that STP could inhibit ADP-induced platelet aggregation, and the inhibitory ratio was 91.50% at the STP concentration of 4.0 mg/mL. Furthermore, STP markedly affected AA metabolism by decreasing the synthesis of MDA (P < 0.01) and increasing the synthesis of 6-keto-PGF(1 alpha), thus changing the plasma TXB2/6-keto-PGF(1 alpha) balance when the platelets were activated (P < 0.01). Therefore, STP altered AA metabolism and these findings

Cloning and characterization of a putative fructosyltransferase and two putative invertase genes from the temperate grass Lolium temulentum L.

J. A. Gallagher, A. J. Cairns and C. J. Pollock (2004). Cloning and characterization of a putative fructosyltransferase and two putative invertase genes from the temperate grass Lolium temulentum L. Journal of Experimental Botany, 55 (397) pp.557-569 Sponsorship: BBSRC RAE2008

Handedness and social anxiety: using Bryden's research as a catalyst to explore the influence of familial sinistrality and degree of handedness

Phil Bryden's work has impacted on many areas of laterality, including degree and measurement of hand preference, as well as influences of familial sinistrality (FS). For example, Bryden[(1977). Measuring handedness with questionnaires. Neuropsychologia, 15, 617–624] is a well-cited and influential paper that remains relevant to this day. Inspired by this we extended our analysis of the relationship between handedness and anxiety in a number of ways. We used familial handedness and strength of handedness to examine their potential influences on anxiety, and extended our research by exploring their relationship to social anxiety, using the Social Phobia Inventory (SPIN). Inconsistent left-handers (ILH) were found to be more socially anxious. In all categories of SPIN except avoidance, ILH were significantly more anxious than consistent right- and left-handers. There were FS differences between ILH with a first degree left-handed relative (FS+) compared to ILH with no first degree left-handed relative (FS−) on all categories of anxiety scores. Within FS+ participants, ILH had significantly higher anxiety scores, compared with consistent handers across all categories. This suggests that ILH's social anxiety may be influenced by a close left-handed relative. Inspired by examining Bryden's work for this special issue, we will continue to add both strength of preference and familial handedness to our work.

Herbal supplements: Recent findings in exercise, health and weight loss

Natural herbs have been in use for weight loss purposes since history began. However, the current global obesity epidemic and the rise in obesity-related chronic diseases, including type-II diabetes and cancer, have highlighted the need for novel and effective approaches for herbal remedies. Whilst the popularity of several prescribed and non-prescribed slimming aids and herbal plant supplements have been marketed for their weight loss efficacy, single and multi-ingredient herbal supplements are still being investigated for their single or combined weight loss benefits. Limited research have highlighted an interesting efficacy for several popular herbal plant supplements including caffeine and capsaicin, Ayurvedic preparations and herbal teas, resulting in various degrees of effectiveness including thermogenic, appetite control and psychological benefits such as mood state. Recent research has suggested acute augmented weight-loss effects of combining herbal ingestion with exercise. For example, ingesting green tea, yerba mate and/or caffeine have been shown to increase metabolic rate, and augmented fatty acid metabolism and to increase energy expenditure from fatty acid sources during exercise with various intensities, particularly at low and moderate intensities. Other promising weight-loss effects have also been also reported for combining exercise with multi-ingredient herbal supplements, particularly those that are rich in phytochemicals and caffeoyl derivatives. Combining herbal ingestions with exercise still require further research in order to establish the supplementation most effective protocols in terms of dosage and timing, and to determine the long-term benefits, particularly those related to exercise protocols, and the long term adherence to sustain the weight loss outcomes.

A study of diet and health in the elderly; the gut microbiota as a source of bioactive agents

The global proportion of older persons is increasing rapidly. Diet and the intestinal microbiota independently and jointly contribute to health in the elderly. The habitual dietary patterns and functional microbiota components of elderly subjects were investigated in order to identify specific effector mechanisms. A study of the dietary intake of Irish community-dwelling elderly subjects showed that the consumption of foods high in fat and/or sugar was excessive, while consumption of dairy foods was inadequate. Elderly females typically had a more nutrient- dense diet than males and a considerable proportion of subjects, particularly males, had inadequate intakes of calcium, magnesium, vitamin D, folate, zinc and vitamin C. The association between dietary patterns, glycaemic index and cognitive function was also investigated. Elderly subjects consuming ‘prudent’ dietary patterns had better cognitive function compared to those consuming ‘Western’ dietary patterns. Furthermore, fully-adjusted regression models revealed that a high glycaemic diet was associated with poor cognitive function, demonstrating a new link between nutrition and cognition. An extensive screening study of the elderly faecal-derived microbiota was also undertaken to examine the prevalence of antimicrobial production by intestinal bacteria. A number of previously characterised bacteriocins were isolated (gassericin T, ABP-118, mutacin II, enterocin L-50 and enterocin P) in this study. Interestingly, a Lactobacillus crispatus strain was found to produce a potentially novel antimicrobial compound. Full genome sequencing of this strain revealed the presence of three loci which exhibited varying degrees of homology with the genes responsible for helveticin J production in Lb. helveticus. An additional study comparing the immunomodulatory capacity of ‘viable’ and ‘non-viable’ Bifidobacterium strains found that Bifidobacterium-fermented milks (BFMs) containing ‘non-viable’ cells could stimulate levels of IL-10 and TNF-α in a manner similar to those stimulated by BFMs containing ‘viable’ cells in vitro.