Search

Cranial measurements have been widely used in various studies in wildlife sciences, ranging from understanding predator ecology to wildlife forensics. However, detailed description of morphometry and sexual dimorphism of the skull of gaur Bos gaurus gaurus is lacking. The present study was undertaken to determine the sexual dimorphism based on the cranial measurements of gaur. A total of 12 individual gaur skulls of male (n = 6) and female (n = 6) were studied in the field from the naturally deceased animals between January 2018 and December 2021 in different ranges of Bandhavgarh tiger reserve (BTR), Madhya Pradesh, India. The skull measurements were analysed using univariate and multivariate statistics to determine whether cranial dimensions could be used to differentiate male and female skulls reliably. A total of 43 morphometrical parameters grouped into nine indices were calculated. Select morphometrical parameters viz PL, GFL, AKI, LBB, LFB, GBEE, GBAN, BPOP and GTCH were significantly different (p < 0.05) between sexes, whereas GBAN were significantly higher in female skulls. The measurements demonstrated that the skull of the gaur was dolichocephalic as the profile length and the otion to otion breath in both male and female were <75% of the length. Overall, 28 linear measurements of both the sexes were statistically significant (p < 0.05; <0.01). The calculated indices revealed that the foramen magnum index in the female gaur were significantly higher. In calculated cranial indices the facial index (a) was higher in female and facial index (b) were higher in males. The two important parameters, facial breadth in facial index (a) and the greatest breadth in facial index (b) were positively correlated, though facial index (a) was statistically not significant between the sexes. The greater inner length of the foramen magnum in female skull resulted in foramen being oval whereas it was circular in males. These parameters were decisive for sexual dimorphism, skull comparison and craniological studies. This study ascertained that the frontal index and skull index had no significant influence and were not good indices for discriminating skulls between male and female. Based on the Principal Component Analysis, it was found that skull of male and female gaurs exhibits differences in cranial morphology viz. cranial profile length or total length (PL) and the least inner height of the temporal groove (LIHT). The findings of the present study provide baseline information on various craniometrical measurements of skull of gaur, indices and parameters for sex identification that can be effectively used in understanding sex biased predation ecology, provide base line information to describe variation across its geographic range, and in identifying skulls recovered in wildlife offence cases., (© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)

The present study aimed to understand microplastic (MP) ingestion by five fish species with different feeding habits namely, Schizothorax richardsonii and Crossocheilus latius (herbivore),Cyprinus carpio (omnivore), Tor chelenoid (herbi-omnivore), and Botia horii (carnivore). The fishes were sampled from River Alaknanda (one of the headwaters of River Ganga) patch at Srinagar, Garhwal, Uttarakhand. The fish gut samples were digested with 30% hydrogen peroxide and vacuum filtered through glass microfiber filter. Each filter paper was observed microscopically to count MPs, and then, selected MPs were chemically characterized using Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR). The results revealed that all the species were contaminated with MPs and the rate of MP ingestion varied with feeding habits. The herbi-omnivore fish, Tor chelenoid, was observed to have the highest MP ingestion. Among the analyzed particles, fibers (66%) were the dominant type of MPs. The MPs were chemically characterized as High-Density Polyethylene (HDPE), Polypropylene (PP), and Polyester. This study contributes as a reference for the forthcoming researches, as it is the pioneer work on the ingestion of MP by fishes of a Himalayan River., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The River Ganga has been explored for microplastics (MPs) majorly in the lower or middle course, while the upper course from where the river starts its journey remains untouched. This study investigates the occurrence and distribution of MPs in the river environment (water and sediment) and common fishes inhabiting the upper stretch of River Ganga in the Uttarakhand state of India. A volume-reduce method by using sieve filtration was used to take water and sediment samples from the study area while fish samples were collected using net method. The samples underwent alkali digestion, microscopic examination, and chemical analysis using Fourier Transformed Infrared Spectroscopy (FTIR). An average of 118.5 ± 49.65 particles per 1000 L and 131.5 ± 53.60 particles/kg dry weight were found in water and sediment respectively. While in the fishes, Tor tor, Schizothorax richardsonii, Labeo dero and Gara gotyla gotyla MPs were 53.13 ± 63.77, 36.33 ± 22.34, 15.42 ± 9.33 and 12.63 ± 5.93 particles/individual respectively. A positive correlation was observed between the number of MPs in fish and their body length, weight, and gut weight, while no correlation was found between feeding habit and MP accumulation. The majority of MPs detected were fibers ranging from 100 μm to 1 mm in size. Polymer types varied among water, sediment, and fish samples, with polyethylene (PE) predominant in water, polypropylene (PP) dominant in sediment, and polyethylene terephthalate (PET) and polystyrene (PS) most abundant in fish samples., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Topologically protected magnetic textures are promising candidates for information carriers in future memory devices, as they can be efficiently propelled at very high velocities using current-induced spin torques. These textures-nanoscale whirls in the magnetic order-include skyrmions, half-skyrmions (merons) and their antiparticles. Antiferromagnets have been shown to host versions of these textures that have high potential for terahertz dynamics, deflection-free motion and improved size scaling due to the absence of stray field. Here we show that topological spin textures, merons and antimerons, can be generated at room temperature and reversibly moved using electrical pulses in thin-film CuMnAs, a semimetallic antiferromagnet that is a testbed system for spintronic applications. The merons and antimerons are localized on 180° domain walls, and move in the direction of the current pulses. The electrical generation and manipulation of antiferromagnetic merons is a crucial step towards realizing the full potential of antiferromagnetic thin films as active components in high-density, high-speed magnetic memory devices., (© 2023. The Author(s).)

To analyse the morphological presentation of orofacial clefts, gender, syndromes and systemic anomalies associated with them., This was an epidemiological study performed in the patients who were registered for cleft lip and palate surgeries in our centre. The data was evaluated both retrospectively as well as prospectively., The patients registered from November 2006 to April 2021 were studied. Out of 5276 patients, data of 5004 cases were analysed, rest 272 patients were excluded due to lack of information. Statistical analysis and Chi square test were applied., Cleft deformities were more common in males than females. Cleft lip with palate was the commonest phenotype (52.2%). It was followed by isolated cleft lip (22.9%), isolated cleft palate (22.1%), rare clefts (1.62%) and syndromic clefts (1.18%). Unilateral variants were more frequent than bilateral. In unilateral, left side was more common than the right side. Among bilateral, most of the cases had premaxillary protrusion. In the present study, 3.46% of all the patients had associated anomalies affecting their other organs. Less common cleft phenotypes like microform cleft lip and submucous cleft palate ± bifid uvula showed frequency of 0.62% and 0.64% respectively., Thorough examination of cleft deformity should be done as it may appear as an isolated deformity or part of a syndrome and have associated systemic anomalies. This may help us to deliver comprehensive care to the patients and can prevent potential operative complications.

Plastic wastes in the environment ultimately reach to the aquatic habitats and become available to aquatic organisms. The pathway of microplastic in aquatic ecosystem is very less investigated specially in freshwater. There have been evidences of MPs ingestion by freshwater biota but the fate of these MPs further in the food chain is unexplored. Thus, we reviewed the status of MPs in freshwater biota and tried to compare the studies to merge the available information, concepts, and perspectives in order to draw a conclusion on bioaccumulation potential, trophic transfer possibilities, biomagnification, and trends of ingesting MPs by the biota. In this review, the previously available information about MPs in aquatic biota is arranged, analyzed, and interpreted to understand all possible routes of MPs in freshwater habitats. The review further provides a better understanding about the lack of information and research gaps that are needed to be explored to develop a solution to the problem of MPs in near future., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Microplastics (MPs) are ubiquitous in our environment. Its presence in air, water, and soil makes it a serious threat to living organisms and has become a critical challenge across ecosystems. Present study aimed to assess the abundance of MPs in aerosols and street dust in Varanasi, a typical urban city in Northern India. Airborne particulates and street dust samples were collected from various sampling sites around Varanasi City. The physical identification of MPs was conducted by binocular microscopy, fluorescence microscopy, and scanning electron microscopy (SEM), while elemental analysis was made by energy-dispersive X-ray (EDX). Finally, Fourier-transform infrared spectroscopy (FTIR) was used for chemical characterization of MPs. Presence of MPs in both aerosols and street dust from all selected sampling sites was confirmed, however with varying magnitude. MPs of different colors having the shape of fragments, films, spherules, and fibers were recorded in the study while fragments (42%) in street dust and fibers (44%) dominated in aerosols. Majority of the MPs were < 1 mm in size and were primarily polypropylene, polystyrene, polyethylene, polyethylene terephthalate, polyester, and polyvinyl chloride types. The EDX spectra showed the presence of toxic inorganic contaminants like metallic elements on MPs, especially elements like aluminum, cadmium, magnesium, sodium, and silicon found to adsorb on the MPs. Presence of MPs in the airborne particulates and street dust in Varanasi is reported for the first time, thus initiating further research and call for a source-specific management plan to reduce its impact on human health and environment., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Bidirectional interactions between plastic tumor cells and the microenvironment critically impact tumor evolution and metastatic dissemination by enabling cancer cells to adapt to microenvironmental stresses by switching phenotype. In melanoma, a key determinant of phenotypic identity is the microphthalmia-associated transcription factor MITF that promotes proliferation, suppresses senescence, and anticorrelates with immune infiltration and therapy resistance. What determines whether MITF can activate or repress genes associated with specific phenotypes, or how signaling regulating MITF might impact immune infiltration is poorly understood. Here, we find that MITF binding to genes associated with high MITF is via classical E/M-box motifs, but genes downregulated when MITF is high contain FOS/JUN/AP1/ATF3 sites. Significantly, the repertoire of MITF-interacting factors identified here includes JUN and ATF3 as well as many previously unidentified interactors. As high AP1 activity is a hallmark of MITF Low , invasive, slow-cycling, therapy resistant cells, the ability of MITF to repress AP1-regulated genes provides an insight into how MITF establishes and maintains a pro-proliferative phenotype. Moreover, although β-catenin has been linked to immune exclusion, many Hallmark β-catenin signaling genes are associated with immune infiltration. Instead, low MITF together with Notch signaling is linked to immune infiltration in both mouse and human melanoma tumors., (© 2022 The Authors. Pigment Cell & Melanoma Research published by John Wiley & Sons Ltd.)

Background: Uvula is a delicate structure in comparison with the rest of the palate. During cleft palate repair, surgeons may find it challenging to suture both the hemi-uvulae meticulously with conventional repair technique and achieve satisfactory aesthetic results. We have adopted few surgical steps in conventional uvular repair to make this procedure simpler and more effective in terms of aesthetic outcome., Methods: From 2016 to 2019, 386 patients underwent primary palatoplasty in our centre. Their uvula was repaired with conventional technique with having those modifications. Out of 386, 211 patients were followed for the 6 months postoperatively., Results: The uvular appearance was satisfactory in 82% of the cases. Undesired appearances of uvula were noted as deviated, bifid and small in 1%, 7% and 10% of cases, respectively. In none of the cases, complete dehiscence of the uvula was seen., Conclusion: The authors advocate simple modifications in conventional uvuloplasty to improve uvular aesthetics. This modified uvuloplasty is easy to practice and very promising in achieving an aesthetically desired uvula in cleft palate surgery., Competing Interests: Conflict of interestThe authors declare that they do not have any conflicts of interest., (© The Association of Oral and Maxillofacial Surgeons of India 2020.)

Aim: To develop a nasal conformer for cleft lip repair which should be easily available and economical., Method: We have used 'Luer mount' of the infant feeding tube as a nasal conformer in 14 patients., Result: Follow-up period ranged from 2 weeks to 3 months. Results were satisfactory in all the patients. No significant complications were noticed in any of the patients., Conclusion: This nasal conformer is easy to use and cost-effective. Though it is not as soft as silicon-based nasal stent but, it provides good support for maintaining the shape of nasal cartilage., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest., (© The Association of Oral and Maxillofacial Surgeons of India 2019.)

It is not unusual for the protruding premaxilla to attain an undesirable position after cleft lip repair. Such a premaxilla may lead to considerable problems in facial aesthetics, or oral functions, or both in early childhood. These abnormal premaxillas may produce difficulties in bone grafting and orthodontic treatment in late childhood. In such cases, surgical correction of the premaxilla in childhood is justified. From 2013 to 2018, 11 children, aged 2 to 11 years, had a secondary ostectomy of their premaxilla. A new stabilisation method (developed by us) was used to provide rigid fixation to the premaxilla. The follow up period ranged from 1 - 6 years. The results were satisfactory in all except for a few minor issues in three patients. There was significant improvement in their appearance, oral functions, and most importantly in their quality of life. The need for secondary osteotomy of the premaxilla should always be weighed against its potential complications. The fixation technique described by us, though, provides rigid fixation, but may potentially be associated with a few complications if not practised carefully., (Copyright © 2020 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.)

Aim: To assess the efficacy of double opposing buccal flap in lengthening the soft palate for velopharyngeal insufficiency correction, and its potential complications in different age groups., Case Series: From March 2016 to June 2019, 50 patients (24 children, 12 adolescents and 14 adults) underwent palatal lengthening using double opposing buccinator myomucosal flaps. Postoperative complications were assessed by two surgeons and the speech outcomes were evaluated by two speech-language pathologists after assessing changes in the hypernasality and intelligibility using a scoring approach. Following the procedure, mild-to-moderate surgical complications were seen, mostly among the adults. There was a significant improvement in hypernasality and intelligibility in all the groups. None of the patients showed hyponasal speech postoperatively., Conclusion: To conclude, the double opposing buccal flap technique is an effective and safe surgical treatment option for the management of velopharyngeal insufficiency in all age groups of patients., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)

In synchronous primary premaxillary setback and cleft lip repair for bilateral cases with severely protruding premaxilla, stabilization of the premaxilla is mostly achieved by gingivoperiosteoplasty. This kind of repair carries risk of impairment of blood supply to the premaxilla and/or prolabium, and at the same time it cannot ensure adequate stabilization of the premaxilla postoperatively. To overcome these problems, we have developed a unique technique of fixation of the premaxilla. In this paper, we discussing this technique, its advantages, and potential complications associated with it. From 2016, 10 patients aged 4-10 months, with bilateral cleft lip and palate with premaxillary protrusion (≥10 mm) underwent premaxillary setback and cheilorhinoplasty in the same stage. Instead of gingivoperiosteoplasty, a 'lag screw' fixation technique was used to stabilize the premaxilla. The follow-up period ranged between 5 and 32 months. In all the cases, we achieved adequate stabilization of the premaxilla. None of the patients had any issue related to the vascularity of the premaxilla or prolabium. There was no impairment in the eruption process of deciduous teeth in the premaxillary segment. Overall aesthetic outcomes of the lip and nose were acceptable. This technique of premaxillary fixation with lag screw gives us the liberty to perform primary cheilorhinoplasty along with premaxillary setback in the same stage, without risking the vascularity of premaxilla and prolabium. It ensures adequate stabilization of the premaxilla, but evaluation of regular growth of the midface and, if needed, corrective orthodontic and surgical treatment in the follow-up periods are advisable., (Copyright © 2019. Published by Elsevier Ltd.)

Introduction: Ectopic eruptions of a tooth in a non-dentate region is a rare entity and such cases have been reported to occur in the nasal cavity, orbital floor, maxillary sinus, mandibular condyle, chin, palate and coronoid process., Case Presentation: We report a case of bilateral ectopic eruption of maxillary third molars associated dentigerous cyst. A 27 years old female patient reported to us with chief complaint of purulent discharge form nose and recurrent facial swelling for last 2 years. Complete removal of cystic lining and extraction of ectopic maxillary third molars along with mandibular third molars was carried out., Results: Post-operative healing was uneventful., Discussion: Bilateral ectopic eruptions of maxillary third molars in Antrum of Highmore (Maxillary sinus) are rarely seen and scantly documented in the literature. Dental ectopia may occur in antrum and present with local sino-nasal symptoms attributed to chronic sinusitis. Due to its rarity and lack of consensus over its management, the incidence deserves to be added to the literature & discussed., (Copyright © 2019. Published by Elsevier Ltd.)

Antiferromagnets have several favourable properties as active elements in spintronic devices, including ultra-fast dynamics, zero stray fields and insensitivity to external magnetic fields 1 . Tetragonal CuMnAs is a testbed system in which the antiferromagnetic order parameter can be switched reversibly at ambient conditions using electrical currents 2 . In previous experiments, orthogonal in-plane current pulses were used to induce 90° rotations of antiferromagnetic domains and demonstrate the operation of all-electrical memory bits in a multi-terminal geometry 3 . Here, we demonstrate that antiferromagnetic domain walls can be manipulated to realize stable and reproducible domain changes using only two electrical contacts. This is achieved by using the polarity of the current to switch the sign of the current-induced effective field acting on the antiferromagnetic sublattices. The resulting reversible domain and domain wall reconfigurations are imaged using X-ray magnetic linear dichroism microscopy, and can also be detected electrically. Switching by domain-wall motion can occur at much lower current densities than those needed for coherent domain switching.

The magnetic order in antiferromagnetic materials is hard to control with external magnetic fields. Using x-ray magnetic linear dichroism microscopy, we show that staggered effective fields generated by electrical current can induce modification of the antiferromagnetic domain structure in microdevices fabricated from a tetragonal CuMnAs thin film. A clear correlation between the average domain orientation and the anisotropy of the electrical resistance is demonstrated, with both showing reproducible switching in response to orthogonally applied current pulses. However, the behavior is inhomogeneous at the submicron level, highlighting the complex nature of the switching process in multidomain antiferromagnetic films.

Antiferromagnets are hard to control by external magnetic fields because of the alternating directions of magnetic moments on individual atoms and the resulting zero net magnetization. However, relativistic quantum mechanics allows for generating current-induced internal fields whose sign alternates with the periodicity of the antiferromagnetic lattice. Using these fields, which couple strongly to the antiferromagnetic order, we demonstrate room-temperature electrical switching between stable configurations in antiferromagnetic CuMnAs thin-film devices by applied current with magnitudes of order 10(6) ampere per square centimeter. Electrical writing is combined in our solid-state memory with electrical readout and the stored magnetic state is insensitive to and produces no external magnetic field perturbations, which illustrates the unique merits of antiferromagnets for spintronics., (Copyright © 2016, American Association for the Advancement of Science.)

AHTPDB (http://crdd.osdd.net/raghava/ahtpdb/) is a manually curated database of experimentally validated antihypertensive peptides. Information pertaining to peptides with antihypertensive activity was collected from research articles and from various peptide repositories. These peptides were derived from 35 major sources that include milk, egg, fish, pork, chicken, soybean, etc. In AHTPDB, most of the peptides belong to a family of angiotensin-I converting enzyme inhibiting peptides. The current release of AHTPDB contains 5978 peptide entries among which 1694 are unique peptides. Each entry provides detailed information about a peptide like sequence, inhibitory concentration (IC50), toxicity/bitterness value, source, length, molecular mass and information related to purification of peptides. In addition, the database provides structural information of these peptides that includes predicted tertiary and secondary structures. A user-friendly web interface with various tools has been developed to retrieve and analyse the data. It is anticipated that AHTPDB will be a useful and unique resource for the researchers working in the field of antihypertensive peptides., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

X-linked inhibitor of apoptosis (XIAP) is a member of inhibitor of apoptosis (IAP) family and involved in the suppression of apoptosis in cancer cells. This property makes it a therapeutic target for the cancer therapy. In the present study, we have developed QSAR models using chemical descriptors, fingerprints, principal components, docking energy parameters and similarity-based approach against XIAP. We have achieved correlation (R) of 0.803 with R(2) value of 0.645 at 10-fold cross validation using SMOreg algorithm. We have evaluated these models on independent dataset to ascertain its robustness and achieved correlation (R) of 0.793 with R(2) value of 0.628. Further, we have used these models for the screening of FDA approved drugs and drug-like molecules from ZINC database and prioritized them on the basis of their predicted pIC50 values. Docking studies of top hits with XIAP-BIR3 domain shows that Iodixanol (DB01249) and ZINC68678304 have higher binding affinities than well-known tetrapeptide inhibitor, AVPI. We have integrated these models in a web server named as "XIAPin". We hope that this web server will contribute in the designing of nifty antagonists against XIAP.

Overexpression of EGFR is responsible for causing a number of cancers, including lung cancer as it activates various downstream signaling pathways. Thus, it is important to control EGFR function in order to treat the cancer patients. It is well established that inhibiting ATP binding within the EGFR kinase domain regulates its function. The existing quinazoline derivative based drugs used for treating lung cancer that inhibits the wild type of EGFR. In this study, we have made a systematic attempt to develop QSAR models for designing quinazoline derivatives that could inhibit wild EGFR and imidazothiazoles/pyrazolopyrimidines derivatives against mutant EGFR. In this study, three types of prediction methods have been developed to design inhibitors against EGFR (wild, mutant and both). First, we developed models for predicting inhibitors against wild type EGFR by training and testing on dataset containing 128 quinazoline based inhibitors. This dataset was divided into two subsets called wild&#95;train and wild&#95;valid containing 103 and 25 inhibitors respectively. The models were trained and tested on wild&#95;train dataset while performance was evaluated on the wild&#95;valid called validation dataset. We achieved a maximum correlation between predicted and experimentally determined inhibition (IC50) of 0.90 on validation dataset. Secondly, we developed models for predicting inhibitors against mutant EGFR (L858R) on mutant&#95;train, and mutant&#95;valid dataset and achieved a maximum correlation between 0.834 to 0.850 on these datasets. Finally, an integrated hybrid model has been developed on a dataset containing wild and mutant inhibitors and got maximum correlation between 0.761 to 0.850 on different datasets. In order to promote open source drug discovery, we developed a webserver for designing inhibitors against wild and mutant EGFR along with providing standalone (http://osddlinux.osdd.net/) and Galaxy (http://osddlinux.osdd.net:8001) version of software. We hope our webserver (http://crdd.osdd.net/oscadd/ntegfr/) will play a vital role in designing new anticancer drugs.

Glycosylation is one of the most abundant and an important post-translational modification of proteins. Glycosylated proteins (glycoproteins) are involved in various cellular biological functions like protein folding, cell-cell interactions, cell recognition and host-pathogen interactions. A large number of eukaryotic glycoproteins also have therapeutic and potential technology applications. Therefore, characterization and analysis of glycosites (glycosylated residues) in these proteins is of great interest to biologists. In order to cater these needs a number of in silico tools have been developed over the years, however, a need to get even better prediction tools remains. Therefore, in this study we have developed a new webserver GlycoEP for more accurate prediction of N-linked, O-linked and C-linked glycosites in eukaryotic glycoproteins using two larger datasets, namely, standard and advanced datasets. In case of standard datasets no two glycosylated proteins are more similar than 40%; advanced datasets are highly non-redundant where no two glycosites' patterns (as defined in methods) have more than 60% similarity. Further, based on our results with several algorihtms developed using different machine-learning techniques, we found Support Vector Machine (SVM) as optimum tool to develop glycosite prediction models. Accordingly, using our more stringent and non-redundant advanced datasets, the SVM based models developed in this study achieved a prediction accuracy of 84.26%, 86.87% and 91.43% with corresponding MCC of 0.54, 0.20 and 0.78, for N-, O- and C-linked glycosites, respectively. The best performing models trained on advanced datasets were then implemented as a user-friendly web server GlycoEP (http://www.imtech.res.in/raghava/glycoep/). Additionally, this server provides prediction models developed on standard datasets and allows users to scan sequons in input protein sequences.

The oilseed Brassica juncea is an important crop with a long history of cultivation in India and China. Previous studies have suggested a polyphyletic origin of B. juncea and more than one migration from the primary to secondary centers of diversity. We investigated molecular genetic diversity based on 99 simple sequence repeat markers in 119 oilseed B. juncea varieties from China, India, Europe, and Australia to test whether molecular differentiation follows Vavilov's proposal of secondary centers of diversity in India and China. Two distinct groups were identified by markers in the A genome, and the same two groups were confirmed by markers in the B genome. Group 1 included accessions from central and western India, in addition to those from eastern China. Group 2 included accessions from central and western China, as well as those from northern and eastern India. European and Australian accessions were found only in Group 2. Chinese accessions had higher allelic diversity per accession (Group 1) and more private alleles per accession (Groups 1 and 2) than those from India. The marker data and geographic distribution of Groups 1 and 2 were consistent with two independent migrations of B. juncea from its center of origin in the Middle East and neighboring regions along trade routes to western China and northern India, followed by regional adaptation. Group 1 migrated further south and west in India, and further east in China, than Group 2. Group 2 showed diverse agroecological adaptation, with yellow-seeded spring-sown types in central and western China and brown-seeded autumn-sown types in India.

Despite the tremendous progress in the field of drug designing, discovering a new drug molecule is still a challenging task. Drug discovery and development is a costly, time consuming and complex process that requires millions of dollar and 10-15 years to bring new drug molecules in the market. This huge investment and long-term process are attributed to high failure rate, complexity of the problem and strict regulatory rules, in addition to other factors. Given the availability of 'big' data with ever improving computing power, it is now possible to model systems which is expected to provide time and cost effectiveness to drug discovery process. Computer Aided Drug Designing (CADD) has emerged as a fast alternative method to bring down the cost involved in discovering a new drug. In past, numerous computer programs have been developed across the globe to assist the researchers working in the field of drug discovery. Broadly, these programs can be classified in three categories, freeware, shareware and commercial software. In this review, we have described freeware or open-source software that are commonly used for designing therapeutic molecules. Major emphasis will be on software and web services in the field of chemo- or pharmaco-informatics that includes in silico tools used for computing molecular descriptors, inhibitors designing against drug targets, building QSAR models, and ADMET properties.

Tumor homing peptides are small peptides that home specifically to tumor and tumor associated microenvironment i.e. tumor vasculature, after systemic delivery. Keeping in mind the huge therapeutic importance of these peptides, we have made an attempt to analyze and predict tumor homing peptides. It was observed that certain types of residues are preferred in tumor homing peptides. Therefore, we developed support vector machine based models for predicting tumor homing peptides using amino acid composition and binary profiles of peptides. Amino acid composition, dipeptide composition and binary profile-based models achieved a maximum accuracy of 86.56%, 82.03%, and 84.19% respectively. These methods have been implemented in a user-friendly web server, TumorHPD. We anticipate that this method will be helpful to design novel tumor homing peptides. TumorHPD web server is freely accessible at http://crdd.osdd.net/raghava/tumorhpd/.

ccPDB (http://crdd.osdd.net/raghava/ccpdb/) is a database of data sets compiled from the literature and Protein Data Bank (PDB). First, we collected and compiled data sets from the literature used for developing bioinformatics methods to annotate the structure and function of proteins. Second, data sets were derived from the latest release of PDB using standard protocols. Third, we developed a powerful module for creating a wide range of customized data sets from the current release of PDB. This is a flexible module that allows users to create data sets using a simple six step procedure. In addition, a number of web services have been integrated in ccPDB, which include submission of jobs on PDB-based servers, annotation of protein structures and generation of patterns. This database maintains >30 types of data sets such as secondary structure, tight-turns, nucleotide interacting residues, metals interacting residues, DNA/RNA binding residues and so on.

ProGlycProt (http://www.proglycprot.org/) is an open access, manually curated, comprehensive repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). To facilitate maximum information at one point, the database is arranged under two sections: (i) ProCGP-the main data section consisting of 95 entries with experimentally characterized glycosites and (ii) ProUGP-a supplementary data section containing 245 entries with experimentally identified glycosylation but uncharacterized glycosites. Every entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. Interestingly, ProGlycProt contains as many as 174 entries for which information is unavailable or the characterized glycosites are unannotated in Swiss-Prot release 2011&#95;07. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology.

Glycosylation is one of the most abundant post-translational modifications (PTMs) required for various structure/function modulations of proteins in a living cell. Although elucidated recently in prokaryotes, this type of PTM is present across all three domains of life. In prokaryotes, two types of protein glycan linkages are more widespread namely, N- linked, where a glycan moiety is attached to the amide group of Asn, and O- linked, where a glycan moiety is attached to the hydroxyl group of Ser/Thr/Tyr. For their biologically ubiquitous nature, significance, and technology applications, the study of prokaryotic glycoproteins is a fast emerging area of research. Here we describe new Support Vector Machine (SVM) based algorithms (models) developed for predicting glycosylated-residues (glycosites) with high accuracy in prokaryotic protein sequences. The models are based on binary profile of patterns, composition profile of patterns, and position-specific scoring matrix profile of patterns as training features. The study employ an extensive dataset of 107 N-linked and 116 O-linked glycosites extracted from 59 experimentally characterized glycoproteins of prokaryotes. This dataset includes validated N-glycosites from phyla Crenarchaeota, Euryarchaeota (domain Archaea), Proteobacteria (domain Bacteria) and validated O-glycosites from phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria (domain Bacteria). In view of the current understanding that glycosylation occurs on folded proteins in bacteria, hybrid models have been developed using information on predicted secondary structures and accessible surface area in various combinations with training features. Using these models, N-glycosites and O-glycosites could be predicted with an accuracy of 82.71% (MCC 0.65) and 73.71% (MCC 0.48), respectively. An evaluation of the best performing models with 28 independent prokaryotic glycoproteins confirms the suitability of these models in predicting N- and O-glycosites in potential glycoproteins from aforementioned organisms, with reasonably high confidence. A web server GlycoPP, implementing these models is available freely at http:/www.imtech.res.in/raghava/glycopp/.

Background: Predicting the function of a protein is one of the major challenges in the post-genomic era where a large number of protein sequences of unknown function are accumulating rapidly. Lectins are the proteins that specifically recognize and bind to carbohydrate moieties present on either proteins or lipids. Cancerlectins are those lectins that play various important roles in tumor cell differentiation and metastasis. Although the two types of proteins are linked, still there is no computational method available that can distinguish cancerlectins from the large pool of non-cancerlectins. Hence, it is imperative to develop a method that can distinguish between cancer and non-cancerlectins., Results: All the models developed in this study are based on a non-redundant dataset containing 178 cancerlectins and 226 non-cancerlectins in which no two sequences have more than 50% sequence similarity. We have applied the similarity search based technique, i.e. BLAST, and achieved a maximum accuracy of 43.25%. The amino acids compositional analysis have shown that certain residues (e.g. Leucine, Proline) were preferred in cancerlectins whereas some other (e.g. Asparatic acid, Asparagine) were preferred in non-cancerlectins. It has been found that the PROSITE domain "Crystalline beta gamma" was abundant in cancerlectins whereas domains like "SUEL-type lectin domain" were found mainly in non-cancerlectins. An SVM-based model has been developed to differentiate between the cancer and non-cancerlectins which achieved a maximum Matthew's correlation coefficient (MCC) value of 0.32 with an accuracy of 64.84%, using amino acid compositions. We have developed a model based on dipeptide compositions which achieved an MCC value of 0.30 with an accuracy of 64.84%. Thereafter, we have developed models based on split compositions (2 and 4 parts) and achieved an MCC value of 0.31, 0.32 with accuracies of 65.10% and 66.09%, respectively. An SVM model based on Position Specific Scoring Matrix (PSSM), generated by PSI-BLAST, was developed and achieved an MCC value of 0.36 with an accuracy of 68.34%. Finally, we have integrated the PROSITE domain information with PSSM and developed an SVM model that has achieved an MCC value of 0.38 with 69.09% accuracy., Conclusion: BLAST has been found inefficient to distinguish between cancer and non-cancerlectins. We analyzed the protein sequences of cancer and non-cancerlectins and identified interesting patterns. We have been able to identify PROSITE domains that are preferred in cancer and non-cancerlectins and thus provided interesting insights into the two types of proteins. The method developed in this study will be useful for researchers studying cancerlectins, lectins and cancer biology. The web-server based on the above study, is available at http://www.imtech.res.in/raghava/cancer&#95;pred/

An elongated styloid process is an unusual source of craniofacial and cervical pain. This condition is characterized by a dull, nagging pharyngeal pain and a palpatory finding in the tonsillar fossa. Eagle described it for the first time in 1937 as Eagle's Syndrome and divided it into two subtypes: the "classic syndrome" and the "stylo-carotid syndrome." The syndrome generally follows tonsillectomy or trauma. Diagnosis is confirmed by radiological findings. Palpation of the styloid process in the tonsillar fossa and infiltration with anesthetic are also used for making a diagnosis. This article presents a case report of a patient with a history of throat pain that was relieved after surgical treatment.

Broomrape (Orobanche aegyptiaca Pers.), an important obligate root parasitic weed in India, has a wide host range including several members of the Solanaceae, Leguminaceae, and Brassicaceae families, among others. Orobanche plants produce thousands of tiny seeds (250 × 300 μm), which can remain viable in the soil for as long as 13 years (3). Rapeseed-mustard (Brassica spp.) is one of the major oilseed crops in India, cultivated on 5.77 million ha with 6.59 million t produced during 2009-2010. Broomrape has been observed in India as a major angiospermic parasitic plant on rapeseed-mustard, tobacco, tomato, and potato. During a field visit to an experimental farm at the Directorate of Rapeseed-Mustard Research, Bharatpur (27°12'N, 77°27'E) in the winter of 2009-2010, symptoms of wilt disease were observed on Orobanche plants, 32.6% of which had wilted completely following root infection. Initial symptoms appeared as a browning of the flowering stalk with wilting. Direct observation of below ground plant parasite tissues revealed a necrosis starting at the radical and advancing to the collar region that shredded later on. Tissue fragments, excised from the internal portions of the diseased tissue, were surface sterilized with 0.1% HgCl 2 , plated on 2% potato dextrose agar (PDA) adjusted to pH 7.0, and incubated at 22 ± 2°C for 7 days. The colonies that grew on PDA plates produced a bright purple color. Single-spore culturing of the fungus yielded Fusarium solani on the basis of morphological characteristics (2). The Fungal Identification Service, Mycology and Plant Pathology Group, Agharkar Research Institute, Pune, India (Accession No. 2156) confirmed the identity. The pathogenicity of the fungus was tested by inoculating five healthy Orobanche plants that were parasitizing Brassica spp. at the radicle region with 10-ml spore suspensions (2 × 10 5 conidia/ml of sterile distilled water) derived from 7-day-old cultures of the fungus. Control plants were treated with sterile distilled water. F. solani-inoculated radicles developed typical wilting symptoms within 2 weeks of treatment, while the control as well as the Brassica spp. plants remained healthy. F. solani was reisolated from inoculated wilted plants, thus fulfilling Koch's postulates. To our knowledge, on the basis of the literature, this is the first report from India showing that F. solani infects O. aegyptica on Brassica spp. There are reports of fungi (50 different species) infecting different hosts in Southern Italy, including F. oxysporum and F. solani, which have been found to be pathogenic to O. ramose. The most pathogenic Fusarium isolates significantly increased the number of dead spikes of broomrape (1). Control of Orobanche spp. poses a challenge because of the lack of effective and economic control measures. F. solani thus offers a potentially promising management strategy that should be explored in the future for the control of O. aegyptiaca. References: (1) A. Boari et al. Biol. Control 30:212, 2004. (2) P. E. Nelson et al. Fusarium Species: An Illustrated Manual for Identification. 1st ed. Pennsylvania State University Press, University Park, 1983. (3) M.C. Press et al. Parasitic Plants. Chapman and Hall, London, UK, 1995.