Development of a Layout-Level Hardware Obfuscation Tool to Counter Reverse Engineering

Reverse engineering of hardware IP block is a common practice for competitive purposes in the semiconductor industry. What is done with the information gathered is the deciding legal factor. Once this information gets into the hands of an attacker, it can be used to manufacture exact clones of the hardware device. In an attempt to prevent the illegal copies of the IP block from flooding the market, layout-level obfuscation based on switchable dopant is suggested for the hardware design. This approach can be integrated into the design and manufacturing flow using an obfuscation tool (ObfusTool) to obfuscate the functionality of the IP core. The ObfusTool is developed in a way to be flexible and adapt to different standard cell libraries and designs. It enables easy and accurate evaluation of the area, power and delay v/s obfuscation trades-offs across different design approaches for hardware obfuscation. The ObfusTool is linked to an obfuscation standard cell library which is based on a prototype design created with Obfuscells and 4-input NAND gate. The Obfuscell is a standard cell which is created with switchable functionality based on the assigned dopant configurations. The Obfuscell is combined with other logic gates to form a standard cell library, which can replace any number of existing gates in the IP block without altering it\u27s functionality. A total of 160 different gates are realized using permutated combinations starting with 26 unique gate functions. This design library provide a high level of obfuscation in terms of the number of combinations an adversary has to go through increase to 2 2000 approximately based on the design under consideration. The connectivity of the design has been ignored by previous approaches, which we have addressed in this thesis. The connectivity of a design leaks important information related to inputs and outputs of a gate. We extend the basic idea of dopant-based hardware obfuscation by introducing dummy wires . The addition of dummy wires not only obfuscates the functionality of the design but also it\u27s connectivity. This greatly reduces the information leakage and complexity of the design increases. To an attacker the whole design appears as one big \u27blob\u27.This also curbs the attempts of brute force attacks. The introduced obfuscation comes at a cost of area and power overhead on an average 5x, which varies across different design libraries

Role of aspiration cytology in splenic lesions

Background: Splenic fine needle aspiration cytology (FNAC) as a diagnostic procedure has been used since beginning of last century and was first reported in 1916. The objective of the study was to evaluate the diagnostic role of aspiration cytology in splenic lesions.Methods: In our retrospective study Fine needle aspiration cytology (FNAC) of spleen was done in a total 34 cases, out of which 28 cases were aspirated under ultrasonological guidance and 6 cases were aspirated blindly. There were 23 male and 11 female patients and the age range of the patients was from 2 to 69 years with 8 patients from paediatric group. Before commencing the procedure all the necessary precautions and investigations including coagulation profile were done.Results: Out of 34 FNAC cases, 5 were bloody aspirate while 2 cases showed normal splenic aspirate. In 27 cases definite diagnostic opinion was possible. Amongst non-neoplastic group maximum patients (8 cases) were showing features of extra medullary hematopoeisis followed by 4 cases of tuberculosis, then 3 cases each of kala azar and storage disorder and 2 cases showed granulomas. In the neoplastic group, we had 2 cases of non-Hodgkins lymphoma, one case of Hodgkin lympoma with 2 cases of hairy cell leukemia and one case of histiocytosis. No major difference in the cellularity noticed when the aspiration done blindly or under ultrasound guidance No procedural complications were seen in our study.Conclusion: Hence when done with full precautions FNAC spleen is a safe, cheap, rapid and highly diagnostic procedure as a primary investigation.

Rrd1p, an RNA polymerase II-specific prolyl isomerase and activator of phosphoprotein phosphatase, promotes transcription independently of rapamycin response.

Rrd1p (resistance to rapamycin deletion 1) has been previously implicated in controlling transcription of rapamycin-regulated genes in response to rapamycin treatment. Intriguingly, we show here that Rrd1p associates with the coding sequence of a galactose-inducible and rapamycin non-responsive GAL1 gene, and promotes the association of RNA polymerase II with GAL1 in the absence of rapamycin treatment following transcriptional induction. Consistently, nucleosomal disassembly at GAL1 is impaired in the absence of Rrd1p, and GAL1 transcription is reduced in the Δrrd1 strain. Likewise, Rrd1p associates with the coding sequences of other rapamycin non-responsive and inducible GAL genes to promote their transcription in the absence of rapamycin treatment. Similarly, inducible, but rapamycin-responsive, non-GAL genes such as CTT1, STL1 and CUP1 are also regulated by Rrd1p. However, transcription of these inducible GAL and non-GAL genes is not altered in the absence of Rrd1p when the steady-state is reached after long transcriptional induction. Consistently, transcription of the constitutively active genes is not changed in the Δrrd1 strain. Taken together, our results demonstrate a new function of Rrd1p in stimulation of initial rounds of transcription, but not steady-state/constitutive transcription, of both rapamycin-responsive and non-responsive genes independently of rapamycin treatment

High mannose-specific lectin Msl mediates key interactions of the vaginal Lactobacillus plantarum isolate CMPG5300

To characterize the interaction potential of the human vaginal isolate Lactobacillus plantarum CMPG5300, its genome was mined for genes encoding lectin-like proteins. cmpg5300.05_29 was identified as the gene encoding a putative mannose-binding lectin. Phenotypic analysis of a gene knock-out mutant of cmpg5300.05_29 showed that expression of this gene is important for auto-aggregation, adhesion to the vaginal epithelial cells, biofilm formation and binding to mannosylated glycans. Purification of the predicted lectin domain of Cmpg5300.05_29 and characterization of its sugar binding capacity confirmed the specificity of the lectin for high-mannose glycans. Therefore, we renamed Cmpg5300.05_29 as a mannose-specific lectin (Msl). The purified lectin domain of Msl could efficiently bind to HIV-1 glycoprotein gp120 and Candida albicans, and showed an inhibitory activity against biofilm formation of uropathogenic Escherichia coli, Staphylococcus aureus and Salmonella Typhimurium. Thus, using a combination of molecular lectin characterization and functional assays, we could show that lectin-sugar interactions play a key role in host and pathogen interactions of a prototype isolate of the vaginal Lactobacillus microbiota

Rad26p regulates the occupancy of histone H2A–H2B dimer at the active genes in vivo

Recently, we have demonstrated a predominant association of Rad26p with the coding sequences but not promoters of several GAL genes following transcriptional induction. Here, we show that the occupancy of histone H2A–H2B dimer at the coding sequences of these genes is not altered following transcriptional induction in the absence of Rad26p. A histone H2A–H2B dimer-enriched chromatin in Δrad26 is correlated to decreased association of RNA polymerase II with the active coding sequences (and hence transcription). However, the reduced association of RNA polymerase II with the active coding sequence in the absence of Rad26p is not due to the defect in formation of transcription complex at the promoter. Thus, Rad26p regulates the occupancy of histone H2A–H2B dimer, which is correlated to the association of elongating RNA polymerase II with active GAL genes. Similar results are also found at other inducible non-GAL genes. Collectively, our results define a new role of Rad26p in orchestrating chromatin structure and hence transcription in vivo

The 19S proteasome subcomplex promotes the targeting of NuA4 HAT to the promoters of ribosomal protein genes to facilitate the recruitment of TFIID for transcriptional initiation in vivo

Previous studies have implicated SAGA (Spt-Ada-Gcn5-acetyltransferase) and TFIID (Transcription factor-IID)-dependent mechanisms of transcriptional activation in yeast. SAGA-dependent transcriptional activation is further regulated by the 19S proteasome subcomplex. However, the role of the 19S proteasome subcomplex in transcriptional activation of the TFIID-dependent genes has not been elucidated. Therefore, we have performed a series of chromatin immunoprecipitation, mutational and transcriptional analyses at the TFIID-dependent ribosomal protein genes such as RPS5, RPL2B and RPS11B. We find that the 19S proteasome subcomplex is recruited to the promoters of these ribosomal protein genes, and promotes the association of NuA4 (Nucleosome acetyltransferase of histone H4) co-activator, but not activator Rap1p (repressor-activator protein 1). These observations support that the 19S proteasome subcomplex enhances the targeting of co-activator at the TFIID-dependent promoter. Such an enhanced targeting of NuA4 HAT (histone acetyltransferase) promotes the recruitment of the TFIID complex for transcriptional initiation. Collectively, our data demonstrate that the 19S proteasome subcomplex enhances the targeting of NuA4 HAT to activator Rap1p at the promoters of ribosomal protein genes to facilitate the recruitment of TFIID for transcriptional stimulation, hence providing a new role of the 19S proteasome subcomplex in establishing a specific regulatory network at the TFIID-dependent promoter for productive transcriptional initiation in vivo

The mRNA cap-binding complex stimulates the formation of pre-initiation complex at the promoter via its interaction with Mot1p in vivo

The cap-binding complex (CBC) binds to the cap structure of mRNA to protect it from exonucleases as well as to regulate downstream post-transcriptional events, translational initiation and nonsense-mediated mRNA decay. However, its role in regulation of the upstream transcriptional events such as initiation or elongation remains unknown. Here, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation assay in conjunction with transcriptional, mutational and co-immunoprecipitational analyses, we show that CBC is recruited to the body of yeast gene, and then stimulates the formation of pre-initiation complex (PIC) at several yeast promoters through its interaction with Mot1p (modifier of transcription). Mot1p is recruited to these promoters, and enhances the PIC formation. We find that CBC promotes the recruitment of Mot1p which subsequently stimulates PIC formation at these promoters. Furthermore, the formation of PIC is essential for recruitment of CBC. Thus, our study presents an interesting observation that an mRNA binding factor exhibits a reciprocal synergistic effect on formation of PIC (and hence transcriptional initiation) at the promoter, revealing a new pathway of eukaryotic gene regulation in vivo

Molecular Study of Mannose Binding Lectin(s) of Lactobacilli and their Potential as HIV Trap

The human body is colonized by a vast number of micro-organisms collectively referred to as the human microbiota. The main microbial niches of the human body include the skin, the oronasopharyngeal cavity, the gastrointestinal tract (GIT) and the genital tract. The microbes in these niches provide various health benefits to the host. Whilst the role of GIT microbiota is well studied in the past few decades, studies on the beneficial effects of vaginal microbiota are limited. Lactobacilli are the most dominant members of the vaginal microbiome playing a crucial role in female health. However, the molecular mechanisms behind the adaptation of these microbes in the vaginal niche and their health promoting effectsare in general not well known. Residing at the site of entry of variouspathogens causing urogenital and sexually transmitted infections, like HIV and Candida, these bacteria play an indispensable role in supportinghost defense.In this PhD research work, we focused on the presence of cell surface-associated mannose binding lectins (MBLs) in vaginal Lactobacillus strains as putative important adaptive and probiotic factors,especially for the design and selection of probiotics to inhibit HIV infection. MBLs constitute a class of carbohydrate binding agents (CBAs) that can bind to mannose rich envelope glycoprotein, gp120, of HIV-1 and related macromolecules exposed on sugar-rich pathogens, and prevent their entry in the host cell. Our first goal was to screen various lactobacilli for the presence of MBLs that could interact with HIV-1 gp120. The screening study revealed only one strain L. plantarum CMPG5300 that boundexclusively to gp120. This strain also exhibited a high degree of auto-aggregation. This vaginal strain was subjected to a genomic and proteomic analysis to search for the putative HIV-1 gp120 binding lectin(s).During genomic analysis, we focused on the annotation of the surface proteome of L. plantarum CMPG5300, in particular candidate genes encoding putative MBL(s) and niche adaptation factors. Sortase dependent proteins (SDPs) form a major class of bacterial surface proteins in these Gram positive bacteria. To investigate if SDP(s) are involved in the gp120 binding capacity of the strain, the sortase gene of CMPG5300 was knocked outusing an optimized electroporation protocol. We observed that the mutant lost its capacity to bind to mannan and HIV-1 gp120. Interestingly, the mutant also became defective in its auto-aggregating property, adhesion to vaginal epithelial cell line and biofilm formation. To investigate the role of the first detected sortase-targeted lectin 1 in gp120 binding of the strain, we constructed a knock-out mutant and also expressed lectin 1 and some of its separate domains in E. coli and we could find some interesting gp120 binding properties.On the other hand, a proteomic analysis was conducted by isolating various protein fractions of CMPG5300. The fractions were separated via affinity chromatography on a mannose-rich sepharose column to elute the MBL(s) of the strain. The chromatographic assays yielded the extracellular form of a moonlighting protein of CMPG5300 as one of the mannose binding adhesins of CMPG5300. This moonlighting protein could however not be purified from supernatant in sufficient amounts. Heterologous expression inside E. coli also did not result in a protein that could bind HIV-1 gp120. However, the recombinant form showed a slight antiviral activity against HIV-2.To conclude, we have identified the auto-aggregating vaginal L. plantarum strain CMPG5300, which shows binding to mannan and the HIV-1 gp120. We could molecularly identify the cell-bound protein lectin 1 and an extracellular released moonlighting protein as putative novel carbohydrate binding agents, but future studies need to further investigate the probiotic potential of CMPG5300, including the ability of the bacterium to lower levels of HIV transmission and infection in vivo.status: publishe

Bilateral, Elongated Styloid Process in A Dry Skull; its Clinical Implications: A Case Report

The styloid process of temporal bone is a slender, elongated, conical bony projection that lies anteromedial to the mastoid process. Its length normally varies from 2-3 cm, and a styloid process longer than 3 cm is found in 4 to 7% of the population. During the routine osteological study of the skull, we came across a skull with bilateral elongated styloid process. The length of the process on the right side was 5.3cm and on the left 5.2cm and the thickness around the base was 1cm bilaterally. The elongated styloid process is recognised as one of the causes of pain in the cranio-cervical region and is one of the causes of Eagle’s syndrome. Eagle syndrome, or elongated styloid process syndrome, is associated with such symptoms as chronic facial and neck pain, dysphagia, tinnitus, referred pain in the ear, glossopharyngeal neuralgia, orbital pain, and radiating pain in the maxillary regions, which worsen when the head rotates or the tonsillar fossa region is palpated. Awareness about an elongated styloid process is important for otolaryngologists, radiologists, surgeons and dentists