MDOT State Study 316 - Development of Advanced Landslide Investigation Protocol Using Geophysical Methods for Mississippi [Cover Title]

SPR-2020-00(001)/108365-1011000Slope failures frequently occur in highway embankments in Mississippi due to the existence of highly expansive Yazoo Clay. In addition, the Mississippi climate, especially the high volume of precipitation, plays a major role in the development of landslides. State Study 316 was undertaken to evaluate the landslides throughout the states employing Advanced Geophysical and Near Surface Remote Sensing tools such as electrical resistivity imaging (ERI), LiDAR technology, and drone imaging. These tools were utilized to identify failed areas, determine their depth, and evaluate crucial soil parameters such as moisture content. Six repaired highway slopes were monitored to collect data on in-situ moisture content, matric suction, temperature variations, and deformation to evaluate their long-term performance. Additionally, ERI, LiDAR, drone imaging, and other advanced investigations were conducted on 20 failed slope sites to evaluate the causes and mechanism failure. The results of the ERI testing showed that shallower depths had higher resistivity values due to unsaturated soil, cracks, displaced disturbed soils, and air pockets that increased the air void ratio. The DEMs generated from drone imagery helped estimate the amount of displaced soil, identify the depth of the slip surface, and recreate failure conditions using numerical modeling tools. The stacked surface profiles developed from the LiDAR point cloud showed details of extreme surficial movement and helped accurately quantify the settlement. The DEMs and the surface profiles can be used as baseline data for future comparisons. Adopting these advanced tools for future research will significantly advance the quality of site investigations and increase the reliability of the design of transportation GEO infrastructures in Mississippi

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

Ground Water Pollution and Emerging Environmental Challenges of Industrial Effluent Irrigation: A Case Study of Mettupalayam Taluk, Tamilnadu

Industrial disposal of effluents on land and the subsequent pollution of groundwater and soil of surrounding farmlands – is a relatively new area of research. The environmental and socioeconomic aspects of industrial effluent irrigation have not been studied as extensively as domestic sewage based irrigation practices, at least for a developing country like India. The disposal of effluents on land has become a regular practice for some industries. Industries located in Mettupalayam Taluk, Tamil Nadu, dispose their effluents on land, and the farmers of the adjacent farmlands have complained that their shallow open wells get polluted and also the salt content of the soil has started building up slowly. This study attempts to capture the environmental and socioeconomic impacts of industrial effluent irrigation in different industrial locations at Mettupalayam Taluk, Tamil Nadu, through primary surveys and secondary information. This study found that the continuous disposal of industrial effluents on land, which has limited capacity to assimilate the pollution load, has led to groundwater pollution. The quality of groundwater in shallow open wells surrounding the industrial locations has deteriorated, and the application of polluted groundwater for irrigation has resulted in increased salt content of soils. In some locations drinking water wells (deep bore wells) also have a high concentration of salts. Since the farmers had already shifted their cropping pattern to salt-tolerant crops (like jasmine, curry leaf, tobacco, etc.) and substituted their irrigation source from shallow open wells to deep bore wells and/or river water, the impact of pollution on livelihoods was minimized. Since the local administration is supplying drinking water to households, the impact in the domestic sector has been minimized. It has also been noticed that in some locations industries are supplying drinking water to the affected households. However, if the pollution continues unabated it could pose serious problems in the future

Development of Soil Moisture Content and Soil Matric Suction Model Based on Field Instrumentation and Electrical Resistivity Imaging (ERI) for Highway Slopes Constructed on High Expansive Clay Soil

In highway slopes (HWS) constructed on high expansive clay soil (HECS), in situ moisture variation is an environmentally driven variable that can significantly impact the safety of the constructed soil. Electrical resistivity imaging (ERI) is a non-destructive method with a considerable potential for subsurface soil moisture mapping, which can be correlated with volumetric soil moisture content (VSMC) and soil matric suction (SMS) of HECS to remarkably enhance the evaluation of the performance of the HWS. However, limited datasets are available to evaluate the accuracy and feasibility of the available correlative field-based models for the HECS under various field conditions. The objective of the current study is to develop a field-based model of VSMC and SMS using real-time field monitoring and ERI data. Six HWS located in the Jackson metro area in Mississippi (MS), USA were considered as reference slopes in this study. Comprehensive field instrumentation was executed at the six HWS to monitor the VSMC, SMS and rainfall intensity. The sensors were installed at the crest, middle and toe of the slope. The 2D ERI test was conducted using a dipole–dipole array with multiple electrodes at 5 ft (1.5 m) spacing. The ERI survey was conducted at the crest and middle of the six HWS to image the continuous soil subsurface profile in terms of moisture variation. The developed models indicated a good agreement between instrumented and ERI data. The developed models will facilitate the estimation of VSMC and SMS variations and aid in performance monitoring of the HWS built on HECS such as Yazoo clay

Near-Surface Soil Moisture Characterization in Mississippi’s Highway Slopes Using Machine Learning Methods and UAV-Captured Infrared and Optical Images

Near-surface soil moisture content variation is a major factor in the frequent shallow slope failures observed on Mississippi’s highway slopes built on expansive clay. Soil moisture content variation is monitored generally through borehole sensors in highway embankments and slopes. This point monitoring method lacks spatial resolution, and the sensors are susceptible to premature failure due to wear and tear. In contrast, Unmanned/Uncrewed Aerial Vehicles (UAVs) have higher spatial and temporal resolutions that enable more efficient monitoring of site conditions, including soil moisture variation. The current study focused on developing two methods to predict soil moisture content (θ) using UAV-captured optical and thermal combined with machine learning and statistical modeling. The first method used Red, Green, and Blue (RGB) color values from UAV-captured optical images to predict θ. Support Vector Machine for Regression (SVR), Extreme Gradient Boosting (XGB), and Multiple Linear Regression (MLR) models were trained and evaluated for predicting θ from RGB values. The XGB model and MLR model outperformed the SVR model in predicting soil moisture content from RGB values. The R2 values for the XGB and MLR models were >0.9 for predicting soil moisture when compared to SVR (R2 = 0.25). The Root Mean Square Error (RMSE) for XGB, SVR, and MLR were 0.009, 0.025, and 0.01, respectively, for the test dataset, affirming that XGB was the best-performing model among the three models evaluated, followed by MLR and SVR. The better-performing XGB and MLR models were further validated by predicting soil moisture using unseen input data, and they provided good prediction results. The second method used Diurnal Land Surface Temperature variation (ΔLST) from UAV-captured Thermal Infrared (TIR) images to predict θ. TIR images of vegetation-covered areas and bare ground areas of the highway embankment side slopes were processed to extract ΔLST amplitudes. The underlying relationship between soil surface thermal inertia and moisture content variation was utilized to develop a predictive model. The resulting single-parameter power curve fit model accurately predicted soil moisture from ΔLST, especially in vegetation-covered areas. The power curve fit model was further validated on previously unseen TIR, and it predicted θ with an accuracy of RMSE = 0.0273, indicating good prediction performance. The study was conducted on a field scale and not in a controlled environment, which aids in the generalizability of the developed predictive models

Crystal structure of Bfr A from Mycobacterium tuberculosis: incorporation of selenomethionine results in cleavage and demetallation of haem

Emergence of tuberculosis as a global health threat has necessitated an urgent search for new antitubercular drugs entailing determination of 3-dimensional structures of a large number of mycobacterial proteins for structure-based drug design. The essential requirement of ferritins/bacterioferritins (proteins involved in iron storage and homeostasis) for the survival of several prokaryotic pathogens makes these proteins very attractive targets for structure determination and inhibitor design. Bacterioferritins (Bfrs) differ from ferritins in that they have additional noncovalently bound haem groups. The physiological role of haem in Bfrs is not very clear but studies indicate that the haem group is involved in mediating release of iron from Bfr by facilitating reduction of the iron core. To further enhance our understanding, we have determined the crystal structure of the selenomethionyl analog of bacterioferritin A (SeMet-BfrA) from Mycobacterium tuberculosis (Mtb). Unexpectedly, electron density observed in the crystals of SeMet-BfrA analogous to haem location in bacterioferritins, shows a demetallated and degraded product of haem. This unanticipated observation is a consequence of the altered spatial electronic environment around the axial ligands of haem (in lieu of Met52 modification to SeMet52). Furthermore, the structure of Mtb SeMet-BfrA displays a possible lost protein interaction with haem propionates due to formation of a salt bridge between Arg53-Glu57, which appears to be unique to Mtb BfrA, resulting in slight modulation of haem binding pocket in this organism. The crystal structure of Mtb SeMet-BfrA provides novel leads to physiological function of haem in Bfrs. If validated as a drug target, it may also serve as a scaffold for designing specific inhibitors. In addition, this study provides evidence against the general belief that a selenium derivative of a protein represents its true physiological native structure

Primary plasmablastic lymphoma of the central nervous system in an immunocompetent man: A case report and review of literature

Plasmablastic lymphoma (PBL) is an aggressive non-Hodgkin lymphoma classically occurring in individuals infected with human immunodeficiency virus (HIV). It has a predilection for the oral cavity and jaw. However, recent case reports have shown this variety of lymphoma in the stomach, lung, nasal cavity, cervical lymph nodes and jejunum in HIV-negative individuals. In this manuscript we report a case of primary PBL of brain in an HIV-negative heterosexual man, who presented with multiple episodes of seizures and hemiparesis. It proved a diagnostic challenge as initial stereotactic brain biopsy showed only few necrotic fragments and possibility of glioblastoma multiforme was rendered. Later patient underwent craniotomy and subsequent histopathology combined with immunohistochemistry led us in making a correct diagnosis of extramedullary PBL. Extensive systemic work up failed to reveal any disease outside the central nervous system. Only single case of primary PBL of brain in HIV-negative individual has been reported until date. To the best of our knowledge, this is the second report to suggest such an association