Resource conversion: a generalizable mechanism for resource-mediated positive species interactions

Positive species interactions are ubiquitous in natural communities, but the mechanisms through which they operate are poorly understood. One proposed mechanism is resource conversion – the conversion by a benefactor species of a resource from a resource state that is inaccessible to a potential beneficiary species into a resource state that is accessible. Such conversion often occurs as a byproduct of resource consumption, and sometimes in exchange for non-resource benefits to the benefactor species. At least five known classes of interactions, including both facilitative and mutualistic ones, may be classified as resource conversion interactions. We formulated a generalizable mathematical model for resource conversion interactions and examined two model variants that represent processing chain and nurse plant interactions. We examined the conditions under which these conformed to the stress-gradient hypothesis (SGH), which predicts increased interaction benefits in more stressful environments. These yielded four key insights: 1) resource conversion interactions can be positive (towards the resource recipient) only when facilitator-mediated resource conversion is more efficient than the baseline, spontaneous, facilitator-independent resource conversion; 2) the sign of resource conversion interaction outcomes never switches (e.g. from net positive to net negative) with changing levels of resource availability, when all other parameters are kept constant; 3) processing chain interactions at equilibrium can never be positive in a manner that conforms to the SGH; 4) nurse plant interactions can be positive and conform to the SGH, although the manner in which they do depends largely on how resource stress is defined, and the environmental supply rate of surface soil moisture. The first two insights are likely to be generalizable across all resource conversion interactions. The general agreement of the model with empirical studies suggest that resource conversion is the mechanism underlying the aforementioned interactions, and an ecologically meaningful way of classifying these previously unassociated positive species interactions.     

Sequencing and Characterisation of Complete Mitogenome DNA for Rasbora hobelmani (Cyprinidae) with Phylogenetic Consideration

Journal of Ichthyology - The Kottelat rasbora Rasbora hobelmani is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome...     

The crystal structure of the mycobacterial trehalose monomycolate transport factor A,TtfA, reveals an atypical fold

Trehalose monomycolate (TMM) represents an essential element of the mycobacterial envelope. While synthesized in the cytoplasm, TMM is transported across the inner membrane by MmpL3 but, little is known regarding the MmpL3 partners involved in this process. Recently, the TMM transport factor A (TtfA) was found to form a complex with MmpL3 and to participate in TMM transport, although its biological role remains to be established. Herein, we report the crystal structure of the Mycobacterium smegmatis TtfA core domain. The phylogenetic distribution of TtfA homologues in non-mycolate containing bacteria suggests that TtfA may exert additional functions.     

Immobilization rapidly selects for chemoresistant ovarian cancer cells with enhanced ability to enter dormancy

Around 20–30% of ovarian cancer patients exhibit chemoresistance, but there are currently no methods to predict whether a patient will respond to chemotherapy. Here, we discovered that chemoresistant ovarian cancer cells exhibit enhanced survival in a quiescent state upon experiencing the stress of physical confinement. When immobilized in stiff silica gels, most ovarian cancer cells die within days, but surviving cells exhibit hallmarks of single-cell dormancy. Upon extraction from gels, the cells resume proliferation but demonstrate enhanced viability upon reimmobilization, indicating that initial immobilization selects for cells with a higher propensity to enter dormancy. RNA-seq analysis of the extracted cells shows they have signaling responses similar to cells surviving cisplatin treatment, and in comparison to chemoresistant patient cohorts, they share differentially expressed genes that are associated with platinum-resistance pathways. Furthermore, these extracted cells demonstrate greater resistance to cisplatin and paclitaxel, despite being proliferative. In contrast, serum starvation and hypoxia could not effectively select for chemoresistant cells upon removal of the environmental stress. These findings demonstrate that ovarian cancer chemoresistance and the ability to enter dormancy are linked, and immobilization rapidly distinguishes chemoresistant cells. This platform could be suitable for mechanistic studies, drug development, or as a clinical diagnostic tool.     

Genetic analysis of ORF5 porcine reproductive and respiratory syndrome virus isolated in Vietnam

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important swine pathogens because it is highly infectious and causes economic losses due to decreased pig productivity. In this study, the 603 bp complete major envelope protein encoding gene (ORF5) of 32 field PRRSV isolates from Vietnam collected during 2008–2012 were sequenced and analyzed. Multiple nucleotide (nt) and deduced amino acid (aa) alignments of ORF5 were performed on the 32 isolates: the representative strains (European and North American genotypes), Chinese strains available in GenBank and vaccine strains licensed for use in Vietnam. The results showed 94.8–100.0% nt identity and 94.0–100% aa similarity among the 32 isolates. These isolates shared similarities with the prototype of the North American PRRSV strain (VR‐2332; nt 87.8–89.3%, aa 87.5–90.0%), and Lelystat virus, the prototype of the European PRRSV strain (LV; nt 61.1–61.9%, aa 55.1‐57.0%). There was greater similarity with QN07 (nt 96.5‐98.5%, aa 96.0‐99.0%) from the 2007 PRRS outbreak in QuangNam Province, CH‐1a (nt 93.2–95.1%, 91.5–93.5%) isolated in China in 1995 and JXA1 (nt 96.5–98.6%, aa 95.0–98.0%), the highly pathogenic strain from China isolated in 2006. The Vietnamese isolates were more similar to JXA1‐R (nt 96.5–98.6%, aa 95.0–98.0%), the strain used in Chinese vaccines, than to Ingelvac MLV/BSL‐PS (nt 87.2–89.0%, aa 86.0–89.0%). Phylogenetic analysis showed that the 32 isolates were of the North American genotype and classified into sub‐lineage 8.7. This sub‐lineage contains highly pathogenic Chinese PRRSV strains. This study documents genetic variation in circulating PRRSV strains and could assist more effective use of PRRS vaccines in Vietnam.     

The J-coupling Restrained Molecular Mechanics (JrMM) Protocol - An Efficient Alternative for Deriving DNA Endocyclic Torsion Angle Constraints Part I: Correlation of Endocyclic Torsion Angles and Vicinal Torsion Angle φ1′2′

Abstract

An efficient alternative which makes use of the reliable ³J_1′2′. value to derive the endocyclic torsion angle constraints is proposed in this study. Based on the information embedded in the two plots, (i) the vicinal proton-proton J-couplings, ³J_1′2′., ³J_1′2″., ³J_2′3′., ³J_2”3′ and ³J_3′4′ against the pseudorotation phase angle, and (ii) ³J_1′2″, ³J_2′3′., ³J_2″3′ and ³J_3′4′ against ³J_1′2′; using the calculated J-couplings obtained for a range of sugar geometries of deoxyribose ring in nucleosides and nucleotides encountered along the pseudorotation itinerary [J. van Wijk, B.D. Huckriede, J.H. Ippel and C. Altona, Methods Enzymol. 211, 286–306 (1992)], it is suggested that the vicinal ³J_1′2′ possesses structural information other than the vicinal torsion angle φ_1′2′. This study is divided into two parts. In Part I, a correlation diagram between the endocyclic torsion angles v_i (i=0,1,2,3,4) and the restrained vicinal torsion angle φ_1′2′ is obtained through the use of the J-coupling restrained molecular mechanics (JrMM) protocol. The established φ_1′2′.-v_i correlation shows v_i can be deduced from the reliable ³J_1′2′. value and it forms the basis for developing an alternative protocol to derive endocyclic torsion angle constraints. In Part II of this series, extensive testing demonstrating the validity of the JrMM protocol to derive V_i for defining the sugar geometry of solution DNA molecules is presented.     

Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium Staphylococcus aureus belonging to the Nit and NitFhit Branch of the nitrilase superfamily

The nitrilases include a variety of enzymes with functional specificities of nitrilase, amidase, and hydrolase reactions. The crystal structure of the uncharacterized protein SA0302 from the pathogenic microorganism Staphylococcus aureus is solved at 1.7?Å resolution. The protein contains 261 amino acids and presents a four-layer αββα sandwich with a chain topology similar to that of a few known CN-hydrolase folds. In the crystal, the proteins are arranged as dimers whose monomers are related by a pseudo twofold rotation symmetry axis. Analysis of the sequences and structures of CN-hydrolases with known 3D structures shows that SA0302 definitely is a member of Branch 10 (Nit and NitFhit) of the nitrilase superfamily. Enzyme activities and substrate specificities of members of this branch are not yet characterized, in contrast to those of the members of Branches 1–9. Although the sequence identities between Branch 10 members are rather low, less than 30%, five conserved regions are common in this subfamily. Three of them contain functionally important catalytic residues, and the two other newly characterized ones are associated with crucial intramolecular and intermolecular interactions. Sequence homology of the area near the active site shows clearly that the catalytic triad of SA0302 is Glu41-Lys110-Cys146. We suggest also that the active site includes a fourth residue, the closely located Glu119. Despite an extensive similarity with other Nit-family structural folds, SA0302 displays an important difference. Protein loop 111–122, which follows the catalytic Lys110, is reduced to half the number of amino acids found in other Nit-family members. This leaves the active site fully accessible to solvent and substrates. We have identified conservative sequence motifs around the three core catalytic residues, which are inherent solely to Branch 10 of the nitrilase superfamily. On the basis of these new sequence fingerprints, 10 previously uncharacterized proteins also could be assigned to this hydrolase subfamily.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:19     

Crop residue incorporation negates the positive effect of elevated atmospheric carbon dioxide concentration on wheat productivity and fertilizer nitrogen recovery

Background and purpose

Rapid increases in atmospheric carbon dioxide concentration ([CO₂]) may increase crop residue production and carbon: nitrogen (C:N) ratio. Whether the incorporation of residues produced under elevated [CO₂] will limit soil N availability and fertilizer N recovery in the plant is unknown. This study investigated the interaction between crop residue incorporation and elevated [CO₂] on the growth, grain yield and the recovery of ¹⁵N-labeled fertilizer by wheat (Triticum aestivum L. cv. Yitpi) under controlled environmental conditions.

Methods

Residue for ambient and elevated [CO₂] treatments, obtained from wheat grown previously under ambient and elevated [CO₂], respectively, was incorporated into two soils (from a cereal-legume rotation and a cereal-fallow rotation) 1 month before the sowing of wheat. At the early vegetative stage ¹⁵N-labeled granular urea (10.22 atom%) was applied at 50 kg?N ha^?1 and the wheat grown to maturity.

Results

When residue was not incorporated into the soil, elevated [CO₂] increased wheat shoot (16 %) and root biomass (41 %), grain yield (19 %), total N uptake (4 %) and grain N removal (8 %). However, the positive [CO₂] fertilization effect on these parameters was absent in the soil amended with residue. In the absence of residue, elevated [CO₂] increased fertilizer N recovery in the plant (7 %), but when residue was incorporated elevated [CO₂] decreased fertilizer N recovery.

Conclusions

A higher fertilizer application rate will be required under future elevated [CO₂] atmospheres to replenish the extra N removed in grains from cropping systems if no residue is incorporated, or to facilitate the [CO₂] fertilization effect on grain yield by overcoming N immobilization resulting from residue amendment.     

Inhibition of neuronal nitric oxide synthase activity promotes migration of human‐induced pluripotent stem cell‐derived neural stem cells toward cancer cells

The breakthrough in derivation of human‐induced pluripotent stem cells (hiPSCs) provides an approach that may help overcome ethical and allergenic challenges posed in numerous medical applications involving human cells, including neural stem/progenitor cells (NSCs). Considering the great potential of NSCs in targeted cancer gene therapy, we investigated in this study the tumor tropism of hiPSC‐derived NSCs and attempted to enhance the tropism by manipulation of biological activities of proteins that are involved in regulating the migration of NSCs toward cancer cells. We first demonstrated that hiPSC‐NSCs displayed tropism for both glioblastoma cells and breast cancer cells in vitro and in vivo. We then compared gene expression profiles between migratory and non‐migratory hiPSC‐NSCs toward these cancer cells and observed that the gene encoding neuronal nitric oxide synthase (nNOS) was down‐regulated in migratory hiPSC‐NSCs. Using nNOS inhibitors and nNOS siRNAs, we demonstrated that this protein is a relevant regulator in controlling migration of hiPSC‐NSCs toward cancer cells, and that inhibition of its activity or down‐regulation of its expression can sensitize poorly migratory NSCs and be used to improve their tumor tropism. These findings suggest a novel application of nNOS inhibitors in neural stem cell‐mediated cancer therapy.