'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the ...duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.
•Epidemiological evidence has identified several viral cofactors in HPV-associated cervical and oral carcinomas.•A common feature of viral cofactors in HPV-associated carcinoma is their ability to ...establish lifelong persistent infections.•Viral cofactors in HPV-associated cancer may act through direct infection of tumor cells or indirectly through various mechanisms.
The etiological role of human papillomavirus (HPV) in anogenital tract and head and neck cancers is well established. However, only a low percentage of HPV-positive women develop cancer, indicating that HPV is necessary but not sufficient in carcinogenesis. Several biological and environmental cofactors have been implicated in the development of HPV-associated carcinoma that include immune status, hormonal changes, parity, dietary habits, tobacco usage, and co-infection with other sexually transmissible agents. Such cofactors likely contribute to HPV persistent infection through diverse mechanisms related to immune control, efficiency of HPV infection, and influences on tumor initiation and progression. Conversely, HPV co-infection with other factors may also harbor anti-tumor effects. Here, we review epidemiological and experimental studies investigating human immunodeficiency virus (HIV), herpes simplex virus (HSV) 1 and 2, human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), BK virus (BKV), JC virus (JCV), and adeno-associated virus (AAV) as viral cofactors in or therapeutic factors against the development of genital and oral HPV-associated carcinomas.
The brain undergoes a protracted, metabolically expensive maturation process from childhood to adulthood. Therefore, it is crucial to understand how network cost is distributed among different brain ...systems as the brain matures. To address this issue, here we examined developmental changes in wiring cost and brain network topology using resting-state functional magnetic resonance imaging (rsfMRI) data longitudinally collected in awake rats from the juvenile age to adulthood. We found that the wiring cost increased in the vast majority of cortical connections but decreased in most subcortico-subcortical connections. Importantly, the developmental increase in wiring cost was dominantly driven by long-range cortical, but not subcortical connections, which was consistent with more pronounced increase in network integration in the cortical network. These results collectively indicate that there is a non-uniform distribution of network cost as the brain matures, and network resource is dominantly consumed for the development of the cortex, but not subcortex from the juvenile age to adulthood.
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular ...components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
AIM: Establishment of ruminal bacterial community in dairy calves. METHODS AND RESULTS: Rumen bacterial community was analysed on 6 calves bred according to commercial practices from day one to ...weaning at day 83 of age, using 454 16S rRNA‐based pyrosequencing. Samples taken at day 1 did not produce amplicons. Analysis of data revealed a three‐stage implantation process with a progressive but important shift of composition. At day 2, the bacterial community was mainly composed of Proteobacteria (70%) and Bacteroidetes (14%), and Pasteurellaceae was the dominant family (58%). The bacterial community abruptly changed between days 2 and 3, and until day 12, dominant genera were Bacteroides (21%), Prevotella (11%), Fusobacterium (5%) and Streptococcus (4%). From 15 to 83 days, when solid food intake rapidly increased, Prevotella became dominant (42%) and many genera strongly decreased or were no longer detected. A limited number of bacteria genera correlated with feed intake, rumen volatile fatty acids and enzymatic activities. CONCLUSION: The ruminal bacterial community is established before intake of solid food, but solid food arrival in turn shapes this community. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides insight into the establishment of calves’ rumen bacterial community and suggests a strong effect of diet.
Anaplastic lymphoma kinase (Alk) has been proposed to regulate neuronal development based on its expression pattern in vertebrates and invertebrates; however, its function in vivo is unknown. We ...demonstrate that Alk and its ligand Jelly belly (Jeb) play a central role as an anterograde signaling pathway mediating neuronal circuit assembly in the
Drosophila visual system. Alk is expressed and required in target neurons in the optic lobe, whereas Jeb is primarily generated by photoreceptor axons and functions in the eye to control target selection of R1–R6 axons in the lamina and R8 axons in the medulla. Impaired Jeb/Alk function affects layer-specific expression of three cell-adhesion molecules, Dumbfounded/Kirre, Roughest/IrreC, and Flamingo, in the medulla. Moreover, loss of
flamingo in target neurons causes some R8-axon targeting errors observed in
jeb and
Alk mosaic animals. Together, these findings suggest that Jeb/Alk signaling helps R-cell axons to shape their environment for target recognition.
Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced ...environmental gradient in the Jakarta Bay–Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters.
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•Goal: assess changes in composition of eight taxa across an in-to-offshore gradient•Relate changes in composition to cross-shelf variation in substrate and water quality•Cross-shelf variation in taxon composition was globally similar.•There were, however, small-scale differences among taxa.•Inshore sites had depauperate assemblages and very low live coral cover.
The emergence of antibiotic-resistant clinical isolates and the decreased rate of development of new antibiotics are a constant threat to human health. In this context, the therapeutic value of ...mastoparan (MP), a toxin from wasp venom, has been extensively studied. However, since MP shows significant cytotoxic activities, further optimization is needed. Here we evaluated the antimicrobial and cytolytic activities of an MP analog created by Ala-substitution in positions 5 and 8, named I5, R8 mastoparan (I5, R8 MP). We found that I5, R8 MP displayed a broad-spectrum antimicrobial activity against bacteria and fungi (MIC in the range 3–25μM), without being hemolytic or cytotoxic toward HEK-293 cells. In addition, I5, R8 MP-amide was highly potent (MIC=3μM) against antibiotic-resistant bacteria. The interaction with microbial membranes was investigated revealing that I5, R8 MP is able to form an active amphipathic α-helix conformation and to disturb membranes causing lysis and cell death. Based on our findings, we hypothesize that I5, R8 MP follows a mechanism of action similar to that proposed for MP, where the pore-forming activity leads to cell death. Our results indicate that hydrophobic moment modified by amino acid substitution may enhance MP selectivity.
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•Amino acid substitutions enhance MP antimicrobial potency and membrane selectivity.•I5, R8 MP adopts an amphipathic α-helix structure indicated by molecular modeling.•I5, R8 MP affects permeability and membrane potential of bacteria.•High-resolution SEM-FEG images showed bacterial and fungal membrane damage.•I5, R8 MP caused rapid complete killing of E. coli within 15min.
The rapid, broad-spectrum, biofilm-eradicating activity of the combination of 0.01% nitroglycerin, 7% citrate, and 20% ethanol and its potential as a nonantibiotic, antimicrobial catheter lock ...solution (ACLS) were previously reported. Here, a nitroglycerin-citrate-ethanol (NiCE) ACLS optimized for clinical assessment was developed by reducing the nitroglycerin and citrate concentrations and increasing the ethanol concentration. Biofilm-eradicating activity was sustained when the ethanol concentration was increased from 20 to 22% which fully compensated for reducing the citrate concentration from 7% to 4% as well as the nitroglycerin concentration from 0.01% to 0.0015% or 0.003%. The optimized formulations demonstrated complete and rapid (2 h) eradication of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate Staphylococcus aureus (VISA), methicillin-resistant Staphylococcus epidermidis (MRSE), vancomycin-resistant enterococci (VRE), multidrug-resistant (MDR) Pseudomonas aeruginosa, MDR Klebsiella pneumoniae, MDR Enterobacter cloacae, MDR Acinetobacter baumannii, MDR Escherichia coli, MDR Stenotrophomonas maltophilia, Candida albicans, and Candida glabrata biofilms. The optimized NiCE lock solutions demonstrated anticoagulant activities comparable to those of heparin lock solutions. NiCE lock solution was significantly more effective than taurolidine-citrate-heparin lock solution in eradicating biofilms of Staphylococcus aureus and Candida glabrata The optimized, nonantibiotic, heparin-free NiCE lock solution demonstrates rapid broad-spectrum biofilm eradication as well as effective anticoagulant activity, making NiCE a high-quality ACLS candidate for clinical assessment.
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