MBAT: A scalable informatics system for unifying digital atlasing workflows

Background  

Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.     

The phylogeny of the ant tribe Formicini (Hymenoptera: Formicidae) with the description of a new genus

Abstract. The holarctic ant tribe Formicini is revised, the new genus Bajcaridris described, and possible phylogenetic relationships are discussed. The subgenus Iberoformica is synonymized with Formica. A synopsis, diagnosis and keys to the genera are provided.     

Midday depression in photosynthesis: Effect on sucrose-phosphate synthase and ribulose-1,5-bisphosphate carboxylase in leaves of Prosopis juliflora (Swartz) DC

The midday depression in net photosynthetic rate (PN) and stomatal conductance (gs) in Prosopis juliflora was studied in relation to two key enzymes of carbon metabolism. Diurnal gas exchange measurements carried out in autumn on P. juliflora showed a pronounced depression in PN and gs along with a decrease in apparent carboxylation efficiency (CE*) during midday. The activities of sucrose-phosphate synthase (SPS) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) also showed large diurnal fluctuations. Initial RuBPCO activity (that present in vivo) and total activity (fully carbamylated activity) increased gradually with increase in irradiance, in the morning reaching a maximum by 08:00 h. The RuBPCO activity declined sharply during midday due to decrease in initial activity. The drop in the % activation of RuBPCO indicated that the deactivation of RuBPCO was achieved via a decarbamylation mechanism. There was a marked similarity in the diurnal patterns of SPS activity and the PN. During a diurnal rhythm, SPS activity increased after irradiation, reaching a maximum at 08:00 h and then declined during midday. Diurnal fluctuations in SPS activity could be due to the changes in the amount of protein (changes in Vmax) as well as to the changes in kinetic properties (changes in Vlim). Hence the midday decline in photosynthesis is closely associated with the regulation of RuBPCO and SPS activities. This revised version was published online in June 2006 with corrections to the Cover Date.     

Cytoprotective Effect of Recombinant Human Erythropoietin Produced in Transgenic Tobacco Plants

Asialo-erythropoietin, a desialylated form of human erythropoietin (EPO) lacking hematopoietic activity, is receiving increased attention because of its broader protective effects in preclinical models of tissue injury. However, attempts to translate its protective effects into clinical practice is hampered by unavailability of suitable expression system and its costly and limit production from expensive mammalian cell-made EPO (rhuEPO^M) by enzymatic desialylation. In the current study, we took advantage of a plant-based expression system lacking sialylating capacity but possessing an ability to synthesize complex N-glycans to produce cytoprotective recombinant human asialo-rhuEPO. Transgenic tobacco plants expressing asialo-rhuEPO were generated by stably co-expressing human EPO and β1,4-galactosyltransferase (GalT) genes under the control of double CaMV 35S and glyceraldehyde-3-phosphate gene (GapC) promoters, respectively. Plant-produced asialo-rhuEPO (asialo-rhuEPO^P) was purified by immunoaffinity chromatography. Detailed N-glycan analysis using NSI-FTMS and MS/MS revealed that asialo-rhuEPO^P bears paucimannosidic, high mannose-type and complex N-glycans. In vitro cytoprotection assays showed that the asialo-rhuEPO^P (20 U/ml) provides 2-fold better cytoprotection (44%) to neuronal-like mouse neuroblastoma cells from staurosporine-induced cell death than rhuEPO^M (21%). The cytoprotective effect of the asialo-rhuEPO^P was found to be mediated by receptor-initiated phosphorylation of Janus kinase 2 (JAK2) and suppression of caspase 3 activation. Altogether, these findings demonstrate that plants are a suitable host for producing cytoprotective rhuEPO derivative. In addition, the general advantages of plant-based expression system can be exploited to address the cost and scalability issues related to its production.     

Midday depression in photosynthesis: Effect on sucrose-phosphate synthase and ribulose-1,5-bisphosphate carboxylase in leaves of Prosopis juliflora (Swartz) DC

The midday depression in net photosynthetic rate (PN) and stomatal conductance (gs) in Prosopis juliflora was studied in relation to two key enzymes of carbon metabolism. Diurnal gas exchange measurements carried out in autumn on P. juliflora showed a pronounced depression in PN and gs along with a decrease in apparent carboxylation efficiency (CE*) during midday. The activities of sucrose-phosphate synthase (SPS) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) also showed large diurnal fluctuations. Initial RuBPCO activity (that present in vivo) and total activity (fully carbamylated activity) increased gradually with increase in irradiance, in the morning reaching a maximum by 08:00 h. The RuBPCO activity declined sharply during midday due to decrease in initial activity. The drop in the % activation of RuBPCO indicated that the deactivation of RuBPCO was achieved via a decarbamylation mechanism. There was a marked similarity in the diurnal patterns of SPS activity and the PN. During a diurnal rhythm, SPS activity increased after irradiation, reaching a maximum at 08:00 h and then declined during midday. Diurnal fluctuations in SPS activity could be due to the changes in the amount of protein (changes in Vmax) as well as to the changes in kinetic properties (changes in Vlim). Hence the midday decline in photosynthesis is closely associated with the regulation of RuBPCO and SPS activities.     

Factors determining the midday depression of photosynthesis in trees under monsoon climate

 Field studies of gas exchange of Populus deltoides, Prosopis juliflora and Acacia auriculiformis showed large diurnal changes in net photosynthesis (A) and stomatal conductance (g_s) during autumn. P. deltoides and P. juliflora undergo pronounced midday depression in A and g_s while A. auriculiformis showed a one-peak response. Several factors indicative of photosynthetic performance were found to be reversibly affected during afternoon decline. These include (i) decrease in initial slope of the CO₂ response curve (carboxylation efficiency), (ii) substantial increase in CO₂ compensation point and (iii) decrease in overall quantum yield of photosystem II. The phenomenon can be duplicated in potted plants by simulating a typical daily pattern of PPFD and VPD. It is found that high VPD induces significant decline in A and g_s at moderate temperature and saturating PPFD (800 μmol m^–2 s^–1) whereas these parameters are only marginally affected at high PPFD and low VPD. Fluorescence data show that the tree species under study have a high capacity for safe dissipation of excessive excitation energy. The activation of photorespiration, as evident from an increase in CO₂ compensation point, maintains constant internal CO₂ concentration (C_i) which may aid in minimizing photoinhibition during stomatal closure at midday. In case of P. deltoides and P. juliflora the stomata seem to be quite sensitive to the changes in humidity whereas this does not appear to be essential in case of A. auriculiformis because of its phyllode structure that endows it with mechanisms for conserving water without undergoing large-scale stomatal changes. Received: 16 October 1997 / Accepted: 5 March 1998