Photonic stopbands and light transmission characteristics in GaAs-based three dimensional waveguides with large index contrast

A relatively simple technique to realize a III–V semiconductor based quasi-three-dimensional photonic crystal material with a refractive index contrast ∼2 is described. Fourier transform infrared spectroscopy measurement reveals a stop band between 15 and 20 μm for a sample with scattering center spacing of 6.3 μm. Another narrow transmittance dip is observable in the wavelength range of 1.1–1.58 μm, with an attenuation of 12 dB at 1.18 μm. The relation between transmission T and waveguide length L, as measured by 1.15 μm wavelength light is either T−L−2T−L−2 or T−exp(−L/L0),T−exp(−L/L0), indicating photon localization in the weakly disordered system. © 1999 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70258/2/APPLAB-75-12-1670-1.pd

Fluid detection with photonic crystal-based multichannel waveguides

A simple fluid detection scheme, based on light propagation through linear defect waveguides in photonic crystals, is demonstrated with isopropanol and xylene. The two-channel photonic crystal waveguide sensor is made from a GaAs-based heterostructure. The preferential channeling of light is controlled by the change in the refractive index of the corresponding waveguide branch due to the presence of the inserted fluid in the guide regions only. © 2003 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71026/2/APPLAB-82-8-1143-1.pd

Effect of organic and inorganic nutrients on rice (Oryza sativa var. CO 51) productivity and soil fertility in the Western zone of Tamil Nadu, India

In sustainable agriculture, to ensure high-quality food production, a combination of organic and inorganic nutrient sources are required. During the winter season of 2020, a field experiment was undertaken in the western zone of Tamil Nadu to assess the effects of organics and inorganics on the growth, yield, and soil properties of rice, Oryza sativa var. CO 51. The experiment was framed in Random Block Design (RBD) comprising of 8 treatments viz., Recommended dose of fertilizer Soil Test Crop Response (STCR) approach (T1), RDF 75 % + Farm yard manure @ 12.5 t ha-1 (T2), T2 + Seed treatment with Azospirillum and Phosphobacteria + Soil application of AM fungi (T3), RDF 75 % + Vermicompost @ 5 t ha-1 (T4), T4 + Seed treatment with Azospirillum and Phosphobacteria + Soil application of AM fungi (T5), FYM @ 12.5 t ha-1 + Seed treatment with Azospirillum and Phosphobacteria + Soil application of AM fungi (T6), Vermicompost @ 5 t ha-1+ Seed treatment with Azospirillum and Phosphobacteria + Soil application of AM fungi (T7) and absolute control (T8) , replicated thrice. Among the integrated nutrient management practices, T5 proved its superiority over other treatments with respect to growth and physiological parameters followed by T3. This would have been because of the solubilization of phosphorus in the soil by AM organisms which is made accessible for crop growth. Utilization of biofertilizer enhanced the N availability and solubilized the inaccessible phosphorus, which thus recorded higher N accessibility and better phosphorus uptake when applied along with a recommended dose of fertilizer for rice.

An electrically injected InAs/GaAs quantum-dot photonic crystal microcavity light-emitting diode

An electrically injected InAs/GaAs self-organized quantum-dot photonic crystal microcavity light-emitting diode operating at 1.04 μm is demonstrated. Light–current characteristics are obtained for devices with two- and five-defect period cavities with maximum light output of 0.17 μW measured in the surface-normal direction. Near-field images were also obtained for an injection current of 8.35 mA, showing light confinement within a few periods of the photonic crystal defect microcavity. © 2002 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70407/2/APPLAB-81-20-3876-1.pd

An algorithm to find similar internal sequence repeats

In recent years, identification of sequence patterns has been given immense importance to understand better their significance with respect to genomic organization and evolutionary processes. To this end, an algorithm has been derived to identify all similar sequence repeats present in a protein sequence. The proposed algorithm is useful to correlate the three-dimensional structure of various similar sequence repeats available in the Protein Data Bank against the same sequence repeats present in other databases like SWISS-PROT, PIR and Genome databases

Cloning and characterization of a caesalpinoid (\u3ci\u3eChamaecrista fasciculata\u3c/i\u3e) hemoglobin: The structural transition from a nonsymbiotic hemoglobin to a leghemoglobin

Nonsymbiotic hemoglobins (nsHbs) and leghemoglobins (Lbs) are plant proteins that can reversibly bind O2 and other ligands. The nsHbs are hexacoordinate and appear to modulate cellular concentrations of NO and maintain energy levels under hypoxic conditions. The Lbs are pentacoordinate and facilitate the diffusion of O2 to symbiotic bacteroids within legume root nodules. Multiple lines of evidence suggest that all plant Hbs evolved from a common ancestor and that Lbs originated from nsHbs. However, little is known about the structural intermediates that occurred during the evolution of pentacoordinate Lbs from hexacoordinate nsHbs. We have cloned and characterized a Hb (ppHb) from the root nodules of the ancient caesalpinoid legume Chamaecrista fasciculata. Protein sequence, modeling data, and spectral analysis indicated that the properties of ppHb are intermediate between that of nsHb and Lb, suggesting that ppHb resembles a putative ancestral Lb. Predicted structural changes that appear to have occurred during the nsHb to Lb transition were a compaction of the CD-loop and decreased mobility of the distal His inhibiting its ability to coordinate directly with the heme-Fe, leading to a pentacoordinate protein. Other predicted changes include shortening of the N- and C-termini, compaction of the protein into a globular structure, disappearance of positive charges outside the heme pocket and appearance of negative charges in an area located between the N- and C-termini. A major consequence for some of these changes appears to be the decrease in O2-affinity of ancestral nsHb, which resulted in the origin of the symbiotic function of Lbs

An Algorithm to Find All Identical Motifs in Multiple Biological Sequences

Sequence motifs are of greater biological importance in nucleotide and protein sequences. The conserved occurrence of identical motifs represents the functional significance and helps to classify the biological sequences. In this paper, a new algorithm is proposed to find all identical motifs in multiple nucleotide or protein sequences. The proposed algorithm uses the concept of dynamic programming. The application of this algorithm includes the identification of (a) conserved identical sequence motifs and (b) identical or direct repeat sequence motifs across multiple biological sequences (nucleotide or protein sequences). Further, the proposed algorithm facilitates the analysis of comparative internal sequence repeats for the evolutionary studies which helps to derive the phylogenetic relationships from the distribution of repeats. © 2010 Springer-Verlag

The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study

<p>Introduction: Children presenting for the first time with inflammatory bowel disease (IBD) offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.</p> <p>Patients and Methods: 100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.</p> <p>Results: 129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates). Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae). No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312).</p> <p>Conclusions: This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.</p&gt

Functional analysis of structural variants in single cells using Strand-seq

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations