24,4,8-Trioxa-21-aza-1,3,6(1,2)-tri­benzena-2(2,3)-bicyclo­[3.3.0]octa­na­cyclo­octa­phane

The crystal structure of the title compound, C26H25NO3, was determined as part of an investigation of host–guest and electron donor–acceptor complexes. The oxazole and the pyrrole rings both adopt envelope conformations. The dihedral angle between the two benzene rings directly linked to the oxazole ring is 49.5 (1)°. The crystal structure is stabilized by a C—H⋯π inter­action

Importance of Spin-Orbit Interaction for the Electron Spin Relaxation in Organic Semiconductors

Despite the great interest organic spintronics has recently attracted, there is only a partial understanding of the fundamental physics behind electron spin relaxation in organic semiconductors. Mechanisms based on hyperfine interaction have been demonstrated, but the role of the spin-orbit interaction remains elusive. Here, we report muon spin spectroscopy and time-resolved photoluminescence measurements on two series of molecular semiconductors in which the strength of the spin-orbit interaction has been systematically modified with a targeted chemical substitution of different atoms at a particular molecular site. We find that the spin-orbit interaction is a significant source of electron spin relaxation in these materials

Applicability of calibrated diffuse reflectance spectroscopy models across spatial and temporal boundaries

Diffuse reflectance spectroscopy (DRS) is an emerging soil testing approach. Although several studies have validated the DRS approach, limited efforts are made to assess the applicability of calibrated DRS models on new samples collected at different locations and/or time. To test such spatio-temporal applicability of calibrated DRS models, we collected surface soil samples from 1,112 smallholder farms during 2018 (T2018) and 607 farms during 2021 (T2021) covering seven districts of the Bundelkhand region of central India. The T2018 samples covered 7 development blocks; the T2021 samples were also collected from these blocks but from different sampling locations. Additionally, a new sampling site (Jhansi-Bamour block) was added during 2021 to create an independent test dataset. Collected samples were analysed for 17 soil parameters (basic soil properties, macronutrients, and micronutrients) and spectral reflectance over the visible to near-infrared region. Corresponding soil test crop response (STCR) ratings were also estimated. The Cubist model was calibrated in the T2018 dataset and tested against the T2021 dataset using the coefficient of determination (R2), root-mean-squared error (RMSE), and percentage relative error deviation (PRED) at 30% error threshold as performance statistics. Model applicability was assessed at each block level (site-specific), by dividing the study site into their two geology-specific regions, and by treating the entire dataset as a regional-scale spectral library. Results showed that DRS models calibrated on a finer scale (site-specific) are less efficient in estimating soil parameters in broader scale (geology-specific and regional-scale) test T2021 samples although their STCR ratings may safely be estimated at local scales. When site-specific data were aggregated to broader scales and T2018 dataset was spiked with 20% samples from the T2021 dataset, model performance improved for critical soil parameters such as soil organic carbon (SOC) contents and several plant nutrients and their ratings; application of such large-scale models also improved the estimation accuracy when applied to site-specific datasets. Exchangeable Ca and Mg, clay and SOC contents were frequently well-estimated with R2 values ranging from 0.54 to 0.93. Fine sand was the next best estimated soil property with R2 values in the range of 0.40–0.75. The STCR ratings estimated in the DRS approach matched the wet chemistry-based STCR ratings to the tune of 43 to 100%. Overall, as many as 60% of all new samples could be estimated with more than 70% accuracy for 8 out of 17 parameters. With the DRS approach tested on both spatially- and temporally-independent test datasets and, specifically, with high estimation accuracy of STCR ratings, our results suggest that the DRS approach may safely be used as a viable alternative to conventional soil testing in smallholder farms

Sustainable intensification opportunities for Alfisols and Vertisols landscape of the semi-arid tropics

Land and water management interventions are key to achieving sustainable intensification in the drylands. This study explores opportunities for doing so in Vertisols and Alfisols using 34-year (1976–2009) long-term experimental data. Four cropping systems were evaluated in each soil types with two land form management interventions, i.e., raised beds and flat beds. Surface runoff generated and soil water content in each system were monitored along with crop yields. In Vertisols, maize-chickpea sequential cropping and sorghum+pigeon pea intercropping on raised beds representing an improved practice was followed for 34 years (1976–2009). Sole chickpea and sole sorghum were grown on flat beds as a traditional system during the same period. In Alfisols, groundnut/pigeon pea intercrop and sole sorghum were grown for 5 years (2002–2006) and sorghum/pigeon pea intercrop and sole castor were grown for 3 years (2007–2009) under raised bed and flat bed conditions, respectively. The use of improved practices in Vertisols produced 3–5 times higher yield compared to traditional practices with net returns estimated at US$800–1300/ha/year compared to US$ 90–350/ha/year under the traditional practice. Despite growing an additional crop, chickpea yield under the improved practice was close to the yield obtained from the traditional practice. In Alfisols, raised beds improved crop yields by 15–20% compared to the flat bed method, leading to an additional net return of US$ 80–100/ha/year. Sorghum/pigeon pea intercrop was found to be superior followed by sole castor, groundnut/pigeon pea intercrop and sole sorghum in Alfisols. Hydrological monitoring revealed opportunities to harvest surface runoff, especially in Alfisols, by building low-cost rainwater harvesting structures that can provide life-saving irrigation during dry spells. An interpretive machine learning (IML) approach was used to estimate four response variables (Sorghum equivalent yield; Net Income; Technical Water Productivity, and Economic Water Productivity) using five different predictor variables (i.e., cropping systems, land form, soil order, effective rainfall (Reff= rainfall-runoff), and water regimes (dry, wet, and normal). Results showed that cropping system is the highest mean feature importance for all the productivity parameters followed by effective rainfall. This paper also discusses soil water dynamics, production functions and technical and economic water productivity which could aid in resource optimization and in developing strategies for land, water and crop management interventions with the aim of bridging yield gaps in the semi-arid tropics

Diagnostic challenges within the Bacillus cereus-group: finding the beast without teeth

The Bacillus cereus-group (B. cereus sensu lato) includes common, usually avirulent species, often considered contaminants of patient samples in routine microbiological diagnostics, as well as the highly virulent B. anthracis. Here we describe 16 isolates from 15 patients, identified as B. cereus-group using a MALDI-TOF MS standard database. Whole genome sequencing (WGS) analysis identified five of the isolates as B. anthracis species not carrying the typical virulence plasmids pXO1 and pXO2, four isolates as B. paranthracis, three as B. cereus sensu stricto, two as B. thuringiensis, one as B. mobilis, and one isolate represents a previously undefined species of Bacillus (B. basilensis sp. nov.). More detailed analysis using alternative MALDI-TOF MS databases, biochemical phenotyping, and diagnostic PCRs, gave further conflicting species results. These cases highlight the difficulties in identifying avirulent B. anthracis within the B. cereus-group using standard methods. WGS and alternative MALDI-TOF MS databases offer more accurate species identification, but so far are not routinely applied. We discuss the diagnostic resolution and discrepancies of various identification methods

Structural Ordering of Disordered Ligand-Binding Loops of Biotin Protein Ligase into Active Conformations as a Consequence of Dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of ∼3.5 Å in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M.tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the self-biotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over self-biotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-5′ AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis