Bacterial symbionts of termite gut flagellates: cospeciation and nitrogen fixation in the gut of dry-wood termites

The subject of this thesis is the symbiosis between flagellates and bacteria in the gut of dry-wood termites (Kalotermitidae). In a series of studies, the evolution of devescovinid flagellates and their bacterial symbionts was elucidated, and the physiological basis of the symbiosis was investigated, with a focus on nitrogen fixation. Devescovinid flagellates are the dominant flagellates in the gut of Kalotermitidae. Species-pure suspensions of devescovinid flagellates (Devescovina and Metadevescovina species) from a wide range of termite species in the family Kalotermitidae were isolated with micropipettes. Ribosomal RNA gene sequences of the host flagellates and their bacterial symbionts were obtained using a full-cycle-rRNA approach. Phylogenetic analysis showed that Devescovina spp. present in many species of Kalotermitidae form a monophyletic group. They were consistently associated with a distinct lineage of ectosymbionts, which form a monophyletic group among the Bacteroidales. The well-supported congruence of their phylogenies documented strict cospeciation of flagellates and their ectosymbionts, which were temporarily classified as “Candidatus Armantifilum devescovinae”. Nevertheless, the complete incongruence between the phylogenies of devescovinid flagellates and Kalotermitidae (COII genes) demonstrated horizontal transfer of flagellates among several species of Kalotermitidae. The presence of filamentous “A. devescovinae” on the surface of Devescovina spp. was corroborated with scanning electron microscopy and fluorescent in situ hybridization. However, several Metadevescovina species, which form a sister group of Devescovina spp., did not possess Bacteroidales ectosymbionts. Moreover, a combination of molecular analysis and electron microscopy led to a correction of the previously overestimated diversity of Metadevescovina species in the gut of termite Incisitermes marginipennis. In contrast to the Bacteroidales ectosymbionts, the endosymbionts of Devescovina spp., which belong to the so-called “Endomicrobia” (TG-1 phylum) and consistently colonized the cytoplasm of all flagellates of this group, were clearly polyphyletic. This suggested that they were acquired independently by each host species. The same seems to be true for the Bacteroidales ectosymbionts of the Oxymonas flagellates present in several Kalotermitidae. These ectosymbionts form several distantly related novel lineages in the phylogenetic tree, underscoring the notion that evolutionary histories of flagellate–bacteria symbioses in the termite gut are complex. Kalotermitidae are known to fix large amounts of atmospheric nitrogen, and acetylene reduction assay showed the presence of nitrogenase activity in the gut of these termites. Community fingerprinting of the nitrogenase genes (homologs of nifH) by T-RFLP analysis revealed that a gene encoding an alternative nitrogenase (anfH) of unknown origin was most highly expressed homolog in mRNA-based profiles. Cloning of the nifH homologs from capillary-picked suspensions of Devescovina arta and Snyderella tabogae gave strong evidence that the “A. devescovinae” are the putative carriers of the anfH gene and therefore responsible for most of the nitrogen-fixing activity in the guts of Neotermes castaneus and Cryptotermes longicollis. Despite a high diversity of nifH homologs in gut homogenates, the only other homologs that were expressed belonged to Treponema, Bacteroidales (nifH), and the proteo-cyano group. The gene expression profiles were specific for the termites. The anfH genes were not expressed in termite species that accumulated large amounts of hydrogen (35–45 kPa, microsensor measurements), suggesting a repression of gene expression by high hydrogen partial pressure

THERMODYNAMIC PROPERTIES OF THE UNFOLDED ENSEMBLE OF PROTEINS

A random coil, whose size is determined by its excluded volume, and net energetic interactions with its environment, has served as a representation of the unfolded ensemble of proteins. The work in this thesis involves equilibrium, nuclear magnetic resonance and time-resolved kinetics spectroscopic studies on the unfolded ensemble of BBL, a globally downhill folding 40-residue protein involved the Krebs cycle of E. coli, in its acid-denatured state, and on a sequence-randomized version of this protein. The effect of variability in thermodynamic conditions, such as temperature and the presence of added chaotropes or kosmotropes, on the equilibrium properties and reconfiguration dynamics of the unfolded state, have been deduced in the absence of competition with folding events at low pH. The unfolded ensemble experiences expansion and collapse to varying degrees in response to changes in these conditions. Individual interactions of residues of the protein with the solvent and the cosolvent (direct interactions), and the properties of the solution itself (indirect interactions) are together critical to the unfolded chain's properties and have been quantitatively estimated. Unfolded, protonated BBL can be refolded by tuning the properties of the solvent by addition of kosmotropic salts. Electrostatic interactions turn out to be essential for folding cooperativity, while solvent-mediated changes in the hydrophobic effect can promote structure formation but cannot induce long-range thermodynamic connectivity in the protein. The effect of sequence on the properties of heteropolymers is also tested with a randomized version of BBL's sequence. Chain radii of gyration, and the degree and rate of hydrophobic collapse depend on the composition of the sequence, viz. hydrophilic versus hydrophobic content. However, the ability to maximize stabilizing interactions and adopt compact conformations is more evident in naturally selected protein sequences versus designed heteropolymers. Chain reconfiguration of unfolded BBL takes place in ∼1/(100 ns), in agreement with theoretical estimates of homopolymer collapse rates. The refolding dynamics of salt-refolded BBL in the range of 1/(6 μs) at 320 K, emerge as being independent of the degree of folding or protonation of the chain, a result in keeping with the description of dynamics in BBL as oscillations in a single, smooth harmonic potential well, which only varies in its position and curvature with varying thermodynamic conditions

Foundation System for “ Akshardham” to Control Deformations Related to Probable Liquefaction

The paper presents a system of foundation for 38.0 m high monumental unique structure “ Akhsardham” on bank of “Yamuna” river at Noida ,New Delhi(India). The design is outcome of interaction of ideological requirements of Architects, Seismologist, Geotechnical and Structural engineers, as well as those empirical rules of Vastu- Shastra for religious places. The structure is typical flexible stone monument. It is located on alluvium of “Yamuna” river in seismic Zone IV of Bureau of Indian standards. The preliminary exploration report indicated liquefaction potential and suggested deep foundations. The engineering priests decided against use of steel for the structure expected to exist for 2-3 countries. The authors reviewed soil report, got quick check tests to for analysis of probability of liquefaction. Based on this studies and deliberations with the above agencies evolved economical massive foundation to fulfill requirements without compromising safety. The construction over foundation is in full swing

Application of Case Studies to Practice in Foundation Engineering in India

India has massive developments, urbanization, housing, communication in last decade. The optimization of cost and saving construction time to complete, are now new aspects which geotechnical engineers are facing. Till today the typical design of shallow foundations of structure-buildings, fly over and dams on non-plastic silty fine sand subsoils found in alluvial deposits of state like Uttar Pradesh, Punjab, Gujarat, Bengal and long coastal belt, were designed by age old practice based on soil mechanics of 1948. Such proven practice became BIS codes for design and construction of structural foundations in 1976-81. The common sense and observational approach of Terzaghi (1959) did not confirm such interpretation of Standard Penetration (SP) test. SP test on non – plastic silty sand at 2 to 3 m below ground surface, being loose (Rd \u3c 15%), had permissible bearing capacity for 25 mm settlement (qa25) less than 100 kPa. This required almost double concrete in footings. Vast country with fast growth had more than million structures built/year, saving of RCC would be around 900 million cubic meter/year. The time reduced will be added advantage. Even up to 10m depth, at number of sites N recorded as 5 to 10 blows/30cm, was considered as “loose” to “medium” by the code indicating prima-facie high liquefaction potential under low seismic activity. This phobia did not spare proposed, under construction over years and existing structures from a long process of reinvestigations, consultants opinions and cost. High rise housing at Chennai, Delhi, Surat, monumental structures at Delhi, Agra, Ahmedabad, Kollkata, Panipat, Rajasthan suffered setback and perpetual suspense due to lack of proper interpretation. Some dams under construction like Ukai, Tenughat, barrages in West Bengal, Delhi, unique projects like Akshardham (Delhi) had to be stopped or delayed by suspected liquefaction. Long chain of opinions and additional tests like evaluation of Rd by alternative methods, rechecking of SPT values, blasting test as well as cross bore holes shear wave velocity tests had to be planned to remove notional interpretation. Study proposes to eliminate such decays & cost escalation by providing alternatives. Typical case studies, showing methodology are also illustrated. Authors with professionals (30 numbers) in geotechnical engineering practicing in India formed a TC-16 technical group (Year 2000-2005) to prepare a report on ground characterization by in-situ testing. The final recommendations for interpretation of SP test (N) and DCP test (NC) for non-plastic alluvial deposit, investigated as per IS code are presented in the form of a chart. It gives for observed N or NC at P0’ (effective overburden pressure) the relative density (Rd), ∅’ (angle of shear resistance), E (deformation modulus) and permissible bearing capacity for 40 mm permissible settlement. The chart also indicate likely liquefaction potential at depth for a = 0.1g for preliminary analysis. Typical case studies have been illustrated. The authors advocated bore holes to be supplemented by uncased DCPT adequate in number, to provide recommendation for an area (not point). If results are not satisfying commonsense, check by in-situ tests for Rd, plate load, even prototype test shall be used before resorting to rejection of site or adopting ground improvement. Any recommendation, for probable liquefaction for existing or under construction project, must be checked by proper reinvestigations and interpretation

The Analysis and Extraction of Structure from Organizational Charts

Organizational charts, also known as org charts, are critical representations of an organization's structure and the hierarchical relationships between its components and positions. However, manually extracting information from org charts can be error-prone and time-consuming. To solve this, we present an automated and end-to-end approach that uses computer vision, deep learning, and natural language processing techniques. Additionally, we propose a metric to evaluate the completeness and hierarchical accuracy of the extracted information. This approach has the potential to improve organizational restructuring and resource utilization by providing a clear and concise representation of the organizational structure. Our study lays a foundation for further research on the topic of hierarchical chart analysis

Relook at Foundation Design of RE Structures in Indian Environment Based on Case Study

India has massive infrastructure development plan in next decade. The safety, cost optimization saving construction time is challenges to engineers. The mass communication progress of 11th & 12th five year plans involves design and execution of large number of underpasses/flyovers through out country. The problems faced by adoption of foundation practice in India based on interpretation of BS 8006 / 1995 during execution are analyzed. Though not widely publicized, failures of walls or part of facial block wall are reported. To avoid contract schedules quick remedial measures are adopted, which based on consultants and facilities includes stone columns, lime piles, CC slab cover over foundation trench etc. A relook at entire problem for RE walls or steep slope foundation is reported. The site specific parameters namely construction season, rains during execution, desiccated expansive soils, settlement of parent subsoil for long life, environment – flood ponding are ignored. A sand-gravel 1.5 m pad foundation cannot take above factors in to account. The soil below the pad is rarely evaluated for differential settlement. Cyclically flooded poorly drained geographical areas particularly for long life structures, needs to be looked into. For Indian fast developing zones a common approach is evolved. This includes specific shallow depth exploration of RE wall foundations, environmental data collection of drainage, flooding and settlement analysis. Depth of trench is site specific depending on desiccated depth and permissible settlement. A model profile of subsoil, replaced relatively impervious fill in trench with or without Geofabrics is presented. The relook of site specific factors and control of settlement in present practice is justified by case studies presented

Maternal diet and gut microbiome composition modulate early-life immune development.

In early life, the intestinal mucosa and immune system undergo a critical developmental process to contain the expanding gut microbiome while promoting tolerance toward commensals, yet the influence of maternal diet and microbial composition on offspring immune maturation remains poorly understood. We colonized germ-free mice with a consortium of 14 strains, fed them a standard fiber-rich chow or a fiber-free diet, and then longitudinally assessed offspring development during the weaning period. Unlike pups born to dams fed the fiber-rich diet, pups of fiber-deprived dams demonstrated delayed colonization with Akkermansia muciniphila, a mucin-foraging bacterium that can also use milk oligosaccharides. The pups of fiber-deprived dams exhibited an enrichment of colonic transcripts corresponding to defense response pathways and a peak in Il22 expression at weaning. Removal of A. muciniphila from the community, but maintenance on the fiber-rich diet, was associated with reduced proportions of RORγt-positive innate and adaptive immune cell subsets. Our results highlight the potent influence of maternal dietary fiber intake and discrete changes in microbial composition on the postnatal microbiome assemblage and early immune development

Laparoscopic Partial Cystectomy for Urachal and Bladder Cancer

PURPOSE: To report our initial experiences with laparoscopic partial cystectomy for urachal and bladder malignancy. MATERIALS AND METHODS: Between March 2002 and October 2004, laparoscopic partial cystectomy was performed in 6 cases at 3 institutions; 3 cases were urachal adenocarcinomas and the remaining 3 cases were bladder transitional cell carcinomas. All patients were male, with a median age of 55 years (45-72 years). Gross hematuria was the presenting symptom in all patients, and diagnosis was established with trans-urethral resection bladder tumor in 2 patients and by means of cystoscopic biopsy in the remaining 4 patients. Laparoscopic partial cystectomy was performed using the transperitoneal approach under cystoscopic guidance. In each case, the surgical specimen was removed intact entrapped in an impermeable bag. One patient with para-ureteral diverticulum transitional cell carcinoma required concomitant ureteral reimplantation. RESULTS: All six procedures were completed laparoscopically without open conversion. The median operating time was 110 minutes (90-220) with a median estimated blood loss of 70 mL (50-100). Frozen section evaluations of bladder margins were routinely obtained and were negative for cancer in all cases. The median hospital stay was 2.5 days (2-4) and the duration of catheterization was 7 days. There were no intraoperative or postoperative complications. Final histopathology confirmed urachal adenocarcinoma in 3 cases and bladder transitional cell carcinoma in 3 cases. At a median follow-up of 28.5 months (range: 26 to 44 months), there was no evidence of recurrent disease as evidenced by radiologic or cystoscopic evaluation. CONCLUSIONS: Laparoscopic partial cystectomy in carefully selected patients with urachal and bladder cancer is feasible and safe, offering a promising and minimally invasive alternative for these patients

Adrenocortical carcinoma with contralateral renal metastases and tumor thrombus: A case report

Adrenocortical carcinoma (ACC) is a rare aggressive malignancy. ACC with renal vein or inferior vena cava (IVC) thrombus is very rare. ACC with contralateral renal metastasis with renal vein thrombus has never been reported. Here we report first such case in the literature where a 40-year-old male presented with right flank pain and weight loss. Definitive reoperative diagnosis failed to be established. Intraoperatively, there was right adrenal mass with left renal vein thrombus invading its wall and extending upto IVC. Right adrenalectomy with left radical nephrectomy with thrombectomy was done. On cut specimen, there was a small mass lesion in the left kidney (upper pole). The diagnosis of ACC with left renal metastasis and renal vein tumor thrombus was confirmed by pathological and immune-histochemical examination. We faced various perioperative challenges in our case. Care must be taken in  preoperative diagnostics, intraoperative planning, and postoperative management as ACC may present with contralateral renal metastasis and tumor thrombus.&nbsp