Combining proteomics and bioinformatics to explore novel tegumental antigens as vaccine candidates against Echinococcus granulosus infection

Echinococcus granulosus is the parasite responsible for cystic echinococcosis (CE), an important worldwide-distributed zoonosis. New effective vaccines against CE could potentially have great economic and health benefits. Here, we describe an innovative vaccine design scheme starting from an antigenic fraction enriched in tegumental antigens from the protoscolex stage (termed PSEx) already known to induce protection against CE. We first used mass spectrometry to characterize the protein composition of PSEx followed by Gene Ontology analysis to study the potential Biological Processes, Molecular Functions, and Cellular Localizations of the identified proteins. Following, antigenicity predictions and determination of conservancy degree against other organisms were determined. Thus, nine novel proteins were identified as potential vaccine candidates. Furthermore, linear B cell epitopes free of posttranslational modifications were predicted in the whole PSEx proteome through colocalization of in silico predicted epitopes within peptide fragments identified by matrix-assisted laser desorption/ionization-TOF/TOF. Resulting peptides were termed “clean linear B cell epitopes,” and through BLASTp scanning against all nonhelminth proteins, those with 100% identity against any other protein were discarded. Then, the secondary structure was predicted for peptides and their corresponding proteins. Peptides with highly similar secondary structure respect to their parental protein were selected, and those potentially toxic and/or allergenic were discarded. Finally, the selected clean linear B cell epitopes were mapped within their corresponding 3D-modeled protein to analyze their possible antibody accessibilities, resulting in 14 putative peptide vaccine candidates. We propose nine novel proteins and 14 peptides to be further tested as vaccine candidates against CE.     

Novel PIKK inhibitor antibody-drug conjugates: Synthesis and anti-tumor activity

Novel neolymphostin-based antibody-drug conjugate (ADC) precursors were synthesized either through amide couplings between both cleavable and non-cleavable linkers and neolymphostin derivatives, or through Cu(I)-catalyzed acetylene-azide click cycloadditon between non-cleavable linkers and neolymphostin acetal derivatives. These precursors were site-specifically conjugated to cysteine mutant trastuzumab-A114C to provide neolymphostin-based ADCs. Preliminary in vitro data indicated that the corresponding ADCs were active against HER2-expressing tumor cell lines, thus providing a proof-of-concept for using neolymphostin as ADC-based anticancer agents.     

Reducing the primate pet trade: Actions for primatologists

This commentary emerged from a panel presentation at the International Primatological Society Congress in Nairobi, Kenya, 2018. The goal was to provide regional updates on the status of primate removal from habitat countries, especially for the pet trade, and develop guidelines that could help primatologists address this critical problem. The trade in live primates includes those used as pets, in entertainment, and as subjects of biomedical experimentation, but here we focus on those primates destined for the pet trade. Such transactions are a hugely lucrative business, impacting hundreds of thousands of individuals annually and affecting the survival of wild populations. Being intimately familiar with primate social behavior, life history and biology, primatologists, whether they work with captive or wild primates, are in a unique position to understand the nature of the trade and attempt to counter its effects. In addition to updating the status of the primate pet trade, we provide recommendations that may help primatologists formulate a plan to deal, locally and regionally, with illegal trafficking in live primates. General guidelines include increasing awareness of local customs, policies and laws; developing collaborative research opportunities for local people; engaging in training/informational opportunities; and instructing on how to take action when encountering illegally-trafficked primates.     

Synergistic effects of nutrients and light favor Nostocales over non-heterocystous cyanobacteria

Blooms of Nostocales (Cyanobacteria) are thought to be invading subtropical and temperate water bodies. According to nutrient stoichiometry and physiological differences between cyanobacterial groups, the replacement of non-heterocystous species by Nostocales is favored when dissolved inorganic nitrogen decreases. However, some studies have shown different trends. We used laboratory bioassays to evaluate the concomitant effects of light and nutrient enrichment on phytoplankton assemblages dominated by non-heterocystous filamentous cyanobacteria. Three nutrient conditions (no addition, addition of phosphate, and addition of nitrate and phosphate) and two light intensities (40 and 80 µmol photon m^?2 s^?1) were assayed. Nostocales replaced or co-dominated with non-heterocystous species in all treatments by the end of the study. The shift in community composition towards Nostocales dominance led to an increase in species richness, which suggests that species with different eco-physiological traits may have differential impacts on diversity. The highest saxitoxin concentrations were measured in no addition treatments, which could link production to nutritional stress. Nostocales featured high phenotypic plasticity in terms of changes in average trichome volume and growth rates. These results help to have a better understanding of the conditions under which Nostocales predominance can occur.     

Colitis and colitis-associated cancer are exacerbated in mice deficient for tumor protein 53-induced nuclear protein 1

Tumor protein 53-induced nuclear protein 1 (TP53INP1) is an antiproliferative and proapoptotic protein involved in cell stress response. To address its physiological roles in colorectal cancer and colitis, we generated and tested the susceptibility of Trp53inp1-deficient mice to the development of colorectal tumors induced by injection of the carcinogen azoxymethane followed by dextran sulfate sodium (DSS)-induced chronic colitis. Trp53inp1-deficient mice showed an increased incidence and multiplicity of tumors compared to those of wild-type (WT) mice. Furthermore, acute colitis induced by DSS treatment was more severe in Trp53inp1-deficient mice than in WT mice. Treatment with the antioxidant N-acetylcysteine prevented colitis and colitis-associated tumorigenesis more efficiently in WT mice than in Trp53inp1-deficient mice, suggesting a higher oxidative load in the latter. Consistently, we demonstrated by electron spin resonance and spin trapping that colons derived from deficient mice produced more free radicals than those of the WT during colitis and that the basal blood level of the antioxidant ascorbate was decreased in Trp53inp1-deficient mice. Collectively, these results indicate that the oxidative load is higher in Trp53inp1-deficient mice than in WT mice, generating a more-severe DSS-induced colitis, which favors development of colorectal tumors in Trp53inp1-deficient mice. Therefore, TP53INP1 is a potential target for the prevention of colorectal cancer in patients with inflammatory bowel disease.     

Temperature controls a latitudinal gradient in the proportion of watershed nitrogen exported to coastal ecosystems

Increased export of biologically available nitrogen (N) to the coastal zone is strongly linked to eutrophication, which is a major problem in coastal marine ecosystems (NRC (2000) Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution. National Academy Press, Washington, DC; Bricker et al. (1999) National Estuarine Eutrophication Assessment. Effects of nutrient enrichment in the nation’s estuaries. NOAA-NOS Special Projects Office, Silver Spring, MD). However, not all of the nitrogen input to a watershed is exported to the coast (Howarth et al. (1996) Biogeochemistry 35:75–139; Jordan and Weller (1996) Bioscience 46:655–664). Global estimates of nitrogen export to coasts have been taken to be 25% of watershed input, based largely on northeastern U.S. observations (Galloway et al. (2004) Biogeochemistry 70:153–226; Boyer et al. (2006) Global Biogeochem Cycle 20:Art. No. GB1S91). We applied the N budgeting methodology developed for the International SCOPE Nitrogen project (Howarth et al. (1996) Biogeochemistry 35:75–139; Boyer et al. (2002) Biogeochemistry 57:137–169) to 12 watersheds in the southeastern U.S., and compared them with estimates of N export for 16 watersheds in the northeastern U.S. (Boyer et al. (2002) Biogeochemistry 57:137–169). In southeastern watersheds, average N export was only 9% of input, suggesting the need for downward revision of global estimates. The difference between northern and southern watersheds is not a function of the absolute value of N inputs, which spanned a comparable range and were positively related to export in both cases. Rather, the proportion of N exported was significantly related to average watershed temperature (% N export = 58.41 e^{−0.11 * temperature}; R ² = 0.76), with lower proportionate nitrogen export in warmer watersheds. In addition, we identified a threshold in proportionate N export at 38°N latitude that corresponds to a reported breakpoint in the rate of denitrification at 10–12°C. We hypothesize that temperature, by regulating denitrification, results in increased proportionate N export at higher latitudes. Regardless of the mechanism, these observations suggest that temperature increases associated with future climate change may well reduce the amount of nitrogen that reaches estuaries, which will have implications for coastal eutrophication.     

Intramolecular activation mechanism of the Dictyostelium LRRK2 homolog Roco protein GbpC

GbpC is a large multidomain protein involved in cGMP-mediated chemotaxis in the cellular slime mold Dictyostelium discoideum. GbpC belongs to the Roco family of proteins that often share a central core region, consisting of leucine-rich repeats, a Ras domain (Roc), a Cor domain, and a MAPKKKinase domain. In addition to this core, GbpC contains a RasGEF domain and two cGMP-binding domains. Here, we report on an intramolecular signaling cascade of GbpC. In vitro, the RasGEF domain of GbpC specifically accelerates the GDP/GTP exchange of the Roc domain. Moreover, cGMP binding to GbpC strongly stimulates the binding of GbpC to GTP-agarose, suggesting cGMP-stimulated GDP/GTP exchange at the Roc domain. The function of the protein in vivo was investigated by rescue analysis of the chemotactic defect of gbpC null cells. Mutants that lack a functional guanine exchange factor (GEF), Roc, or kinase domain are inactive in vivo. Together, the results suggest a four-step intramolecular activation mechanism of the Roco protein GbpC: cGMP binding to the cyclic nucleotide-binding domains, activation of the GEF domain, GDP/GTP exchange of Roc, and activation of the MAPKKK domain.     

Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice

Mammalian Genome - Stabilin2 (Stab2) encodes a large transmembrane protein which is predominantly expressed in the liver sinusoidal endothelial cells (LSECs) and functions as a scavenger receptor...     

Watershed nitrogen input and riverine export on the west coast of the US

This study evaluated the sources, sinks, and factors controlling net export of nitrogen (N) from watersheds on the west coast of the US. We calculated input of new N to 22 watersheds for 1992 and 2002. 1992 inputs ranged from 541 to 11,644 kg N km⁻² year⁻¹, with an overall area-weighted average of 1,870 kg N km⁻² year⁻¹. In 2002, the range of inputs was 490–10,875 kg N km⁻² year⁻¹, averaging 2,158 kg N km⁻² year⁻¹. Fertilizer was the most important source of new N, averaging 956 (1992) and 1,073 kg N km⁻² year⁻¹ (2002). Atmospheric deposition was the next most important input, averaging 833 (1992) and 717 kg N km⁻² year⁻¹ (2002), followed by biological N fixation in agricultural lands. Riverine N export, calculated based on measurements taken at the furthest downstream USGS water quality monitoring station, averaged 165 (1992) and 196 kg N km⁻² year⁻¹ (2002), although data were available for only 7 watersheds at the latter time point. Downstream riverine N export was correlated with variations in streamflow (export = 0.94 × streamflow − 5.65, R ² = 0.66), with N inputs explaining an additional 16% of the variance (export = 1.06 × streamflow + 0.06 × input − 227.78, R ² = 0.82). The percentage of N input that is exported averaged 12%. Percent export was also related to streamflow (%export = 0.05 × streamflow − 2.61, R ² = 0.60). The correlations with streamflow are likely a result of its large dynamic range in these systems. However, the processes that control watershed N export are not yet completely understood.