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1.  Inference of the Protokaryotypes of Amniotes and Tetrapods and the Evolutionary Processes of Microchromosomes from Comparative Gene Mapping 
PLoS ONE  2012;7(12):e53027.
Comparative genome analysis of non-avian reptiles and amphibians provides important clues about the process of genome evolution in tetrapods. However, there is still only limited information available on the genome structures of these organisms. Consequently, the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes in tetrapods remain poorly understood. We constructed chromosome maps of functional genes for the Chinese soft-shelled turtle (Pelodiscus sinensis), the Siamese crocodile (Crocodylus siamensis), and the Western clawed frog (Xenopus tropicalis) and compared them with genome and/or chromosome maps of other tetrapod species (salamander, lizard, snake, chicken, and human). This is the first report on the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes inferred from comparative genomic analysis of vertebrates, which cover all major non-avian reptilian taxa (Squamata, Crocodilia, Testudines). The eight largest macrochromosomes of the turtle and chicken were equivalent, and 11 linkage groups had also remained intact in the crocodile. Linkage groups of the chicken macrochromosomes were also highly conserved in X. tropicalis, two squamates, and the salamander, but not in human. Chicken microchromosomal linkages were conserved in the squamates, which have fewer microchromosomes than chicken, and also in Xenopus and the salamander, which both lack microchromosomes; in the latter, the chicken microchromosomal segments have been integrated into macrochromosomes. Our present findings open up the possibility that the ancestral amniotes and tetrapods had at least 10 large genetic linkage groups and many microchromosomes, which corresponded to the chicken macro- and microchromosomes, respectively. The turtle and chicken might retain the microchromosomes of the amniote protokaryotype almost intact. The decrease in number and/or disappearance of microchromosomes by repeated chromosomal fusions probably occurred independently in the amphibian, squamate, crocodilian, and mammalian lineages.
PMCID: PMC3534110  PMID: 23300852
2.  A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization 
BMC Genomics  2009;10(Suppl 2):S9.
Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian.
The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole).
We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
PMCID: PMC2966330  PMID: 19607660
3.  Exhaustive exercise training enhances aerobic capacity in American alligator (Alligator mississippiensis) 
The oxygen transport system in mammals is extensively remodelled in response to repeated bouts of activity, but many reptiles appear to be ‘metabolically inflexible’ in response to exercise training. A recent report showed that estuarine crocodiles (Crocodylus porosus) increase their maximum metabolic rate in response to exhaustive treadmill training, and in the present study, we confirm this response in another crocodilian, American alligator (Alligator mississippiensis). We further specify the nature of the crocodilian training response by analysing effects of training on aerobic [citrate synthase (CS)] and anaerobic [lactate dehydrogenase (LDH)] enzyme activities in selected skeletal muscles, ventricular and skeletal muscle masses and haematocrit. Compared to sedentary control animals, alligators regularly trained for 15 months on a treadmill (run group) or in a flume (swim group) exhibited peak oxygen consumption rates higher by 27 and 16%, respectively. Run and swim exercise training significantly increased ventricular mass (~11%) and haematocrit (~11%), but not the mass of skeletal muscles. However, exercise training did not alter CS or LDH activities of skeletal muscles. Similar to mammals, alligators respond to exercise training by increasing convective oxygen transport mechanisms, specifically heart size (potentially greater stroke volume) and haematocrit (increased oxygen carrying-capacity of the blood). Unlike mammals, but similar to squamate reptiles, alligators do not also increase citrate synthase activity of the skeletal muscles in response to exercise.
PMCID: PMC2768110  PMID: 19533151
Alligator; Citrate synthase; Exercise; Metabolic rate; Oxygen consumption
4.  Diving through the thermal window: implications for a warming world 
Population decline and a shift in the geographical distribution of some ectothermic animals have been attributed to climatic warming. Here, we show that rises in water temperature of a few degrees, while within the thermal window for locomotor performance, may be detrimental to diving behaviour in air-breathing ectotherms (turtles, crocodilians, marine iguanas, amphibians, snakes and lizards). Submergence times and internal and external body temperature were remotely recorded from freshwater crocodiles (Crocodylus johnstoni) while they free-ranged throughout their natural habitat in summer and winter. During summer, the crocodiles' mean body temperature was 5.2 ± 0.1°C higher than in winter and the largest proportion of total dive time was composed of dive durations approximately 15 min less than in winter. Diving beyond 40 min during summer required the crocodiles to exponentially increase the time they spent on the surface after the dive, presumably to clear anaerobic debt. The relationship was not as significant in winter, even though a greater proportion of dives were of a longer duration, suggesting that diving lactate threshold (DLT) was reduced in summer compared with winter. Additional evidence for a reduced DLT in summer was derived from the stronger influence body mass exerted upon dive duration, compared to winter. The results demonstrate that the higher summer body temperature increased oxygen demand during the dive, implying that thermal acclimatization of the diving metabolic rate was inadequate. If the study findings are common among air-breathing diving ectotherms, then long-term warming of the aquatic environment may be detrimental to behavioural function and survivorship.
PMCID: PMC2992703  PMID: 20610433
crocodilian; ectotherm; acclimatization; temperature; aerobic dive limit
5.  Characterization of Serum Phospholipase A2 Activity in Three Diverse Species of West African Crocodiles 
Secretory phospholipase A2, an enzyme that exhibits substantial immunological activity, was measured in the serum of three species of diverse West African crocodiles. Incubation of different volumes of crocodile serum with bacteria labeled with a fluorescent fatty acid in the sn-2 position of membrane lipids resulted in a volume-dependent liberation of fluorescent probe. Serum from the Nile crocodile (Crocodylus niloticus) exhibited slightly higher activity than that of the slender-snouted crocodile (Mecistops cataphractus) and the African dwarf crocodile (Osteolaemus tetraspis). Product formation was inhibited by BPB, a specific PLA2 inhibitor, confirming that the activity was a direct result of the presence of serum PLA2. Kinetic analysis showed that C. niloticus serum produced product more rapidly than M. cataphractus or O. tetraspis. Serum from all three species exhibited temperature-dependent PLA2 activities but with slightly different thermal profiles. All three crocodilian species showed high levels of activity against eight different species of bacteria.
PMCID: PMC3205705  PMID: 22110960
6.  Bio-efficacy of Dioscorea pentaphylla from Midmid-Western Ghats, India 
Toxicology International  2012;19(2):100-105.
Antibacterial and antifungal activity of crude extracts of medicinally important and traditionally used yam plant, Dioscorea pentaphylla, from mid-Western Ghats was evaluated against 27 bacterial and 5 fungal clinical strains collected of the patients from infectious sources. The clinical strains belonging to their respective species showed concentration-dependent susceptibility toward crude petroleum ether extract, chloroform extract and methanol extract at 100 μg/100 μl. The extracts exhibited predominant antibacterial activity against Staphylococcus aureus (ATCC-20852), Pseudomonas aeruginosa (ATCC-29737) and Klebsiella pneumoniae (MTCC-618), respectively, and five clinically isolated pathogenic fungi, Trichophyton rubrum, Microsporum gypseum, Tricophyton tonsurans, Microsporum audouini, and Candida albicans, with antibacterial drug ciprofloxacin and antifungal drug fluconozole (50 μg/100 μl) as standards. Out of the three extracts, ethanol extracts possessed better minimum inhibitory concentration (MIC) against all the bacterial strains. All the three extracts showed significant activity against all the five fungal pathogen strains. The results are promising and support the traditional use of D. pentaphylla for the treatment of bacterial and fungal infections.
PMCID: PMC3388750  PMID: 22778504
Antifungal; antibacterial; Dioscoreapentaphylla; minimum inhibitory concentration
7.  Satellite Tracking Reveals Long Distance Coastal Travel and Homing by Translocated Estuarine Crocodiles, Crocodylus porosus 
PLoS ONE  2007;2(9):e949.
Crocodilians have a wide distribution, often in remote areas, are cryptic, secretive and are easily disturbed by human presence. Their capacity for large scale movements is poorly known. Here, we report the first study of post-release movement patterns in translocated adult crocodiles, and the first application of satellite telemetry to a crocodilian. Three large male Crocodylus porosus (3.1–4.5 m) were captured in northern Australia and translocated by helicopter for 56, 99 and 411 km of coastline, the last across Cape York Peninsula from the west coast to the east coast. All crocodiles spent time around their release site before returning rapidly and apparently purposefully to their capture locations. The animal that circumnavigated Cape York Peninsula to return to its capture site, travelled more than 400 km in 20 days, which is the longest homeward travel yet reported for a crocodilian. Such impressive homing ability is significant because translocation has sometimes been used to manage potentially dangerous C. porosus close to human settlement. It is clear that large male estuarine crocodiles can exhibit strong site fidelity, have remarkable navigational skills, and may move long distances following a coastline. These long journeys included impressive daily movements of 10–30 km, often consecutively.
PMCID: PMC1978533  PMID: 17895990
8.  A genetic linkage map for the saltwater crocodile (Crocodylus porosus) 
BMC Genomics  2009;10:339.
Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary.
A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1).
We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear.
This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly.
PMCID: PMC2907706  PMID: 19640266
9.  Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia 
Mobile DNA  2012;3:20.
Endogenous retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the nuclear DNA of a germ-line cell. Here we present the results of a survey into the ERV complement of Crocodylus porosus, the saltwater crocodile, representing 45 individuals from 17 sampling locations in the Northern Territory of Australia. These retroelements were compared with published ERVs from other species of Crocodylia (Crocodilians; alligators, caimans, gharials and crocodiles) as well as representatives from other vertebrates. This study represents one of the first in-depth studies of ERVs within a single reptilian species shedding light on the diversity of ERVs and proliferation mechanisms in crocodilians.
Analyses of the retroviral pro-pol gene region have corroborated the presence of two major clades of ERVs in C. porosus and revealed 18 potentially functional fragments out of the 227 recovered that encode intact pro-pol ORFs. Interestingly, we have identified some patterns of diversification among those ERVs as well as a novel sequence that suggests the presence of an additional retroviral genus in C. porosus. In addition, considerable diversity but low genetic divergence within one of the C. porosus ERV lineages was identified.
We propose that the ERV complement of C. porosus has come about through a combination of recent infections and replication of ancestral ERVs. Strong purifying selection acting on these clades suggests that this activity is recent or still occurring in the genome of this species. The discovery of potentially functional elements is an interesting development that warrants further investigation.
PMCID: PMC3531266  PMID: 23217152
Crocodylia; Endogenous retrovirus; Crocodylus porosus
10.  In vitro antibacterial evaluation of Anabaena sp. against several clinically significant microflora and HPTLC analysis of its active crude extracts 
Indian Journal of Pharmacology  2010;42(2):105-107.
The present study was conducted to evaluate the possible antibacterial activity of Anabaena extracts. Anabaena was isolated from a natural source and cultured in vitro. after suitable growth, cyanobacterial culture was harvested using different solvents. Extracts, thus prepared, were evaluated for their antibacterial potential by agar-well diffusion assay against bacterial species of clinical significance. MIC values were determined further to check the concentration ranges for significant inhibition. HPTLC analysis was done to separate the components of active crude extract in an attempt to identify the bio-active chemical entity. Methanol extract exhibited more potent activity than that of hexane and ethyl acetate extracts. No inhibitory effect was found against Pseudomonas aeruginosa, Salmonella typhi, and Klebsiella pneumoniae. Staphylococcus aureus required about 256 µg/ml of the crude methanol extract for effective inhibition. HPTLC evaluation at λ 254 nm was performed for the separation of a complex mixture of the methanol extract. The results provide evidence that Anabaena sp. extracts might indeed be potential sources of new antibacterial agents.
PMCID: PMC2907006  PMID: 20711376
Blue-green algae; drug-resistance; biologically active substances; bacterial species
11.  The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny. 
The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups). The analyses corroborated the view that turtles are at the base of the bird-crocodile branch. This position of the turtles makes Diapsida paraphyletic. The origin of the squamates was estimated at 294 million years (Myr) ago and that of the turtles at 278 Myr ago. Phylogenetic analysis of mammalian relationships using the additional outgroups corroborated the Marsupionta hypothesis, which joins the monotremes and the marsupials to the exclusion of the eutherians.
PMCID: PMC1088649  PMID: 11297180
12.  Studies on Pongamia pinnata (L.) Pierre leaves: understanding the mechanism(s) of action in infectious diarrhea*  
While data are available on the effect of medicinal plants on intestinal motility and their antibacterial action, there is a paucity of information on their mode of action on various aspects of diarrheal pathogenicity, namely colonization to intestinal epithelial cells and production/action of enterotoxins. Crude decoction of dried leaves of Pongamia pinnata was evaluated for its antimicrobial (antibacterial, antigiardial and antirotaviral) effect; and its effect on production and action of enterotoxins (cholera toxin, CT; Escherichia coli labile toxin, LT; and E. coli stable toxin, ST); and adherence of enteropathogenic E. coli and invasion of enteroinvasive E. coli and Shigella flexneri to epithelial cells. The decoction had no antibacterial, antigiardial and antirotaviral activity, but reduced production of CT and bacterial invasion to epithelial cells. The observed results indicated that the crude decoction of P. pinnata has selective antidiarrheal action with efficacy against cholera and enteroinvasive bacterial strains causing bloody diarrheal episodes.
PMCID: PMC1533752  PMID: 16845722
Pongamia pinnata; Medicinal plants; Diarrhea; Antidiarrheal agent; Enterotoxin; Colonization
13.  Evaluation of susceptibility of gram-positive and -negative bacteria to human defensins by using radial diffusion assay. 
Antimicrobial Agents and Chemotherapy  1996;40(10):2280-2284.
Defensins are small cationic bactericidal peptides present abundantly in the granules of polymorphonuclear neutrophils (PMNs). Human PMNs contain four defensins termed HNP-1 to HNP-4. We used a new assay system in agar plates, the radial diffusion assay, to evaluate the effects of human defensins against gram-positive and -negative bacteria. A crude mixture of HNP-1, -2, and -3 (crude HNPs) was purified from human PMN extracts by reversed-phase high-pressure liquid chromatography (RP-HPLC). The different components were later separated by RP-HPLC and gel permeation chromatography. We compared the antibacterial activities of purified HNP-1, -2, and -3 against Escherichia coli, Pseudomonas aeruginosa, methicillin-susceptible Staphylococcus aureus, and methicillin-resistant S. aureus strains using the radial diffusion assay. The antibacterial activities of HNP-1 and HNP-2 against all strains tested were similar to those of the crude HNPs, but the activity of HNP-3 was less than those of the other defensins. To quantitate the activities of HNPs against different bacteria, we defined the minimal dose of crude HNPs forming a detectable clear zone around the bacteria as the minimal inhibitory dose (MID) and determined the MIDs for 10 strains of E. coli, 12 strains of P. aeruginosa, 10 strains of methicillin-susceptible S. aureus, and 12 strains of methicillin-resistant S. aureus isolates, including clinical isolates. In general, the MIDs of the HNPs were similar against similar bacterial species. However, the MIDs for P. aeruginosa were higher than those for the other organisms tested. The radial diffusion assay is suitable as a screening test for measuring the susceptibilities of isolates to defensins, because it is sensitive and simple and has good reproducibility.
PMCID: PMC163519  PMID: 8891130
14.  Determinants of Habitat Selection by Hatchling Australian Freshwater Crocodiles 
PLoS ONE  2011;6(12):e28533.
Animals almost always use habitats non-randomly, but the costs and benefits of using specific habitat types remain unknown for many types of organisms. In a large lake in northwestern Australia (Lake Argyle), most hatchling (<12-month-old) freshwater crocodiles (Crocodylus johnstoni) are found in floating vegetation mats or grassy banks rather than the more widely available open banks. Mean body sizes of young crocodiles did not differ among the three habitat types. We tested four potential explanations for non-random habitat selection: proximity to nesting sites, thermal conditions, food availability, and exposure to predation. The three alternative habitat types did not differ in proximity to nesting sites, or in thermal conditions. Habitats with higher food availability harboured more hatchlings, and feeding rates (obtained by stomach-flushing of recently-captured crocodiles) were highest in such areas. Predation risk may also differ among habitats: we were twice as likely to capture a crocodile after seeing it in open-bank sites than in the other two habitat types. Thus, habitat selection of hatchling crocodiles in this system may be driven both by prey availability and by predation risk.
PMCID: PMC3233590  PMID: 22163308
15.  Crocodiles in the Sahara Desert: An Update of Distribution, Habitats and Population Status for Conservation Planning in Mauritania 
PLoS ONE  2011;6(2):e14734.
Relict populations of Crocodylus niloticus persist in Chad, Egypt and Mauritania. Although crocodiles were widespread throughout the Sahara until the early 20th century, increased aridity combined with human persecution led to local extinction. Knowledge on distribution, occupied habitats, population size and prey availability is scarce in most populations. This study evaluates the status of Saharan crocodiles and provides new data for Mauritania to assist conservation planning.
Methodology/Principal Findings
A series of surveys in Mauritania detected crocodile presence in 78 localities dispersed across 10 river basins and most tended to be isolated within river basins. Permanent gueltas and seasonal tâmoûrts were the most common occupied habitats. Crocodile encounters ranged from one to more than 20 individuals, but in most localities less than five crocodiles were observed. Larger numbers were observed after the rainy season and during night sampling. Crocodiles were found dead in between water points along dry river-beds suggesting the occurrence of dispersal.
Research priorities in Chad and Egypt should focus on quantifying population size and pressures exerted on habitats. The present study increased in by 35% the number of known crocodile localities in Mauritania. Gueltas are crucial for the persistence of mountain populations. Oscillations in water availability throughout the year and the small dimensions of gueltas affect biological traits, including activity and body size. Studies are needed to understand adaptation traits of desert populations. Molecular analyses are needed to quantify genetic variability, population sub-structuring and effective population size, and detect the occurrence of gene flow. Monitoring is needed to detect demographical and genetical trends in completely isolated populations. Crocodiles are apparently vulnerable during dispersal events. Awareness campaigns focusing on the vulnerability and relict value of crocodiles should be implemented. Classification of Mauritanian mountains as protected areas should be prioritised.
PMCID: PMC3045445  PMID: 21364897
16.  Isolation and characterization of a bactericidal withanolide from Physalis virginiana 
Pharmacognosy Magazine  2012;8(29):22-28.
Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments.
Materials and Methods:
This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from 1H and 13C NMR and MS.
Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. 1H and 13C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C28H40O6.
An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V.
PMCID: PMC3307198  PMID: 22438659
Antibacterial; cytotoxicity; physagulin V; Physalis virginiana; withanolide
17.  Studies on bioprospecting potential of a gastropod mollusc Cantharus tranquebaricus (Gmelin, 1791) 
To study the biological activities of the tissue extract of Cantharus tranquebaricus (C. tranquebaricus).
Crude extract of gastropod was tested for inhibition of bacterial growth. Antibacterial assay was carried out by disc diffusion method and the activity was measured accordingly based on the inhibition zone around the disc impregnated with gastropod extract. Molecular weight of the extract was determined by using SDS-PAGE. Plasma coagulation, Fibrin plate assay and substrate SDS-PAGE were used to determine the effect of sample on plasma coagulation, fibrin (ogen) olytic and proteolytic activity.
The maximum inhibition zone (10 mm) was observed against Vibrio cholera (V. cholera) and minimum inhibition zone (2 mm) was noticed against Proteus mirablis (P. mirablis). The molecular weight was determined as 47-106 kDa. The tissue extract shows proteolytic activity above 48 kDa. SDS-PAGE analysis of fibrinogen after incubation with the tissue extract showed fibrinogenolytic activity. In plasma coagulation assay C. tranquebaricus tissue extract showed procoagulant property and it coagulated chicken plasma within 150 s, while control took 5 min to clot. The 9 HU hemolytic units were found against chicken blood and also exhibit high level of brine shrimp lethality.
This study suggests that C. tranquebaricus could be used as potential source for isolating bioactive compounds, since it is explored first time and found with promising results.
PMCID: PMC3609219  PMID: 23569843
Antimicrobial; Proteolytic; Fibrinolytic; Hemolytic; Brine shrimp lethality; Cantharus tranquebaricus; Plasma coagulation
18.  Antibacterial activity of the venom of Heterometrus xanthopus 
Indian Journal of Pharmacology  2012;44(4):509-511.
Heterometrus xanthopus (Scorpion) is one of the most venomous and ancient arthropods. Its venom contains anti-microbial peptides like hadrurin, scorpine, Pandinin 1, and Pandinin 2 that are able to effectively kill multidrug-resistant pathogens. The present study was conducted to evaluate the anti-bacterial activity of H. xanthopus venom. Six Gram-positive and Gram-negative bacterial strains were tested against 1/100, 1/10, and 1/1 fractions of distilled water diluted and crude venom. 1/100 and 1/10 dilutions were not successful in any of the six bacterial strains studied while the 1/1 dilution was effective on Bacillus subtilis ATCC 6633, Salmonella typhimurium ATCC 14028, and Pseudomonas aeruginosa ATCC 27853 with highest zone of inhibition were obtained on B. subtilis. Crude venom was effective against Enterococcus faecalis ATCC 14506, B. subtilis, S. typhimurium, and P. aeruginosa. The most effective results were observed on B. subtilis.
PMCID: PMC3469957  PMID: 23087515
Antibiotics; antimicrobial activity; extracts; Heterometrus xanthopus venom
19.  Interactions of Antibiotics and Methanolic Crude Extracts of Afzelia Africana (Smith.) Against Drug Resistance Bacterial Isolates 
Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to discover fresh antimicrobials or new practices that are effective for the treatment of infectious diseases caused by drug-resistant microorganisms. The objective of this experiment is to investigate for synergistic outcomes when crude methanolic extract of the stem bark of Afzelia africana and antibiotics were combined against a panel of antibiotic resistant bacterial strains that have been implicated in infections. Standard microbiological protocols were used to determine the minimum inhibitory concentrations (MICs) of the extract and antibiotics, as well as to investigate the effect of combinations of the methanolic extract of A. africana stem bark and selected antibiotics using the time-kill assay method. The extract of Afzelia africana exhibited antibacterial activities against both Gram-negative and Gram-positive bacteria made up of environmental and standard strains at a screening concentration of 5 mg/mL. The MICs of the crude extracts and the antibiotics varied between 1 μg/mL and 5.0 mg/mL. Overall, synergistic response constituted about 63.79% of all manner of combinations of extract and antibiotics against all test organisms; antagonism was not detected among the 176 tests carried out. The extract from A. africana stem bark showed potentials of synergy in combination with antibiotics against strains of pathogenic bacteria. The detection of synergy between the extract and antibiotics demonstrates the potential of this plant as a source of antibiotic resistance modulating compounds.
PMCID: PMC3155364  PMID: 21845091
Afzelia Africana; synergy; antibiotics; extract; drug-resistant; microorganisms
20.  Screening of biological activities of Polygonum maritimum L. from Algerian coast 
To investigate the antioxidant and the antibacterial activities of crude extract from aerial part of Polygonum maritimum L. (Polygonaceae) (P. maritimum) and to find new actives biomolecules.
The whole plant was collected from the Rechgoune coast (West of Algeria), and methanolic crude extract of aerial parts of P. maritimum (PMCE) was prepared. The extract was tested against different bacterial strain and tested for his ability to neutralize free radical (DPPH) and to scavenge the H2O2.
PMCE had a very high content of total phenol, which was (352.49±18.03) mg/g dry weight, expressed as gallic acid equivalent. PMCE exhibited excellent antioxidant activity, as measured using DPPH and H2O2 scavenging assays. It also showed a high antibacterial activity against gram-positive bacterial strains: Bacillus cereus, Bacillus subtilis and Staphylococcus aureus with an highest MIC of 120 µg/mL.
The antioxidant and antibacterial activity of the PMCE is probably due to phenolic compounds present in the extract. The contemporary presence of antioxidant and antibacterial activities in the PMCE suggests that this plant may be a source of bioactive substances with multifaceted activity.
PMCID: PMC3703553  PMID: 23905017
Polygonum maritimum L.; Phenolic compounds; Antioxidant activity; Antibacterial activity
21.  Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes 
Genome Biology  2012;13(1):415.
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
PMCID: PMC3334581  PMID: 22293439
Genomics; evolution; Crocodylia; Archosauria; amniote
22.  Stress in farmed saltwater crocodiles (Crocodylus porosus): no difference between individually- and communally-housed animals 
SpringerPlus  2013;2:381.
Minimising stress in farmed crocodiles is not only important for improving animal welfare, but may also improve skin blemish healing and infection resistance, which influence the quality of the final skin product. Forty near-harvest size saltwater crocodiles (1.6-1.8 m TL) from two Australian farms were sampled to evaluate the effect of different pen types (communal pens n=20; individual pens n=20) on stress as indicated by plasma corticosterone. Blood samples were taken within three minutes of immobilisation and analysed using a commercial enzyme immunoassay kit. There was no relationship with animal size (P=0.16), between farms (P=0.86), pen types (P=0.69), communal pens between farms (P=0.28) or individual pens between farms (P=0.24). Based on corticosterone levels, it appears that individual pens do not cause significantly more stress on harvest-size animals than communal pens. Individual pens meet their design specifications by achieving comparable healing rates of belly skin blemishes as communal pens without compromising animal welfare and minimising the possibility of new blemishes.
PMCID: PMC3755803  PMID: 24010039
Communal pens; Corticosterone; Individual pens; Saltwater crocodile; Stress
23.  Antibacterial Activities of the Extracts and Conessine from Holarrhena Floribunda G. DON. (Apocynaceae) 
The methanolic extract and conessine isolated from the stem bark of Holarrhena floribunda (Hf) were tested for their antibacterial activities on Bacillus: Bacillus cereus, Bacillus subtilis, Bacillus megaterium and Bacillus stearothermophilus using the disc diffusion method. Phytochemical analysis of the crude extract and fractions was also conducted. The inhibition parameters of the crude methanol extract and the total alkaloid fraction were determined using the macrodilution method. The results showed that the crude extract, the total alkaloid fraction and conessine exhibited a significant antibacterial effect against all the strains studied. The antibacterial effect of conessine is almost similar to that of chloramphenicol used as reference. The ratio of the minimal bactericidal concentration (MBC) over the minimal inhibitive concentration (MIC) indicates the bactericidal effect of the plant. These results support common use of stem bark of Hf and conessine isolated from Hf in the treatment of some infectious diseases.
PMCID: PMC2816488  PMID: 20161899
Antibacterial activities; Holarrhena floribunda; Bacillus; conessine
24.  Antimicrobial activities of the tissue extracts of Babylonia spirata Linnaeus, 1758 (Mollusca: Gastropoda) from Thazhanguda, southeast coast of India 
To investigate the antimicrobial activity of the tissue extracts of Babylonia spirata (B. spirata) against nine bacterial and three fungal pathogens.
Crude extract of gastropod was tested for inhibition of bacterial and fungal growth. Antibacterial assay was carried out by disc diffusion method and in vitro antifungal activity was determined against Czapex Dox agar. The antimicrobial activity was measured accordingly based on the inhibition zone around the disc impregnated with gastropod extract. Molecular size of muscle protein was determined using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). And fourier transform infrared spectroscopy (FTIR) spectro photometry analysis was also studied.
The maximum inhibition zone (12 mm) was observed against Pseudomonas aeruginosa in the crude ethanol extract of B. spirata and the minimum inhibition zone (2 mm) was noticed against Staphylococcus aureus in the crude methanol extract of B. spirata. Water extract of B. spirata showed the highest activity against Vibrio parahaemolyticus, Staphylococcus aureus and Candida albicans. Ethanol, acetone, methanol, chloroform and water extracts showed antimicrobial activity against almost all the bacteria and fungus. Compared with water extracts, ethanol and methanol extracts showed higher activity against all pathogens. The molecular weight of protein of the gastropod sample ranged from 2-110 kDa on SDS-PAGE. FTIR analysis revealed the presence of bioactive compounds signals at different ranges.
The research shows that the great medicinal value of the gastropod muscle of B. spirata may be due to high quality of antimicrobial compounds.
PMCID: PMC3609203  PMID: 23569831
Gastropod; Babylonia spirata; Antimicrobial activity; SDS-PAGE; FTIR; Antibacterial activity; Antifungal activity; Inhibition zone; Muscle protein; Bioactive compound
25.  Apoptosis of human cholangiocarcinoma cells induced by ESC-3 from Crocodylus siamensis bile 
AIM: To investigate the effects of ESC-3 isolated from crocodile bile on the growth and apoptosis induction of human cholangiocarcinoma cells.
METHODS: ESC-3 was isolated from crocodile bile by Sephadex LH-20 and RP-18 reversed-phase column. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay was conducted to determine the effects of ESC-3 on the proliferation of human cholangiocarcinoma cell lines (QBC939, Sk-ChA-1 and MZ-ChA-1). Giemsa staining, Hoechst 33258 and acridine orange/ethidium bromide staining showed the morphological changes of Mz-ChA-1 cells exposed to ESC-3 at different concentrations. Flow cytometry with regular propidium iodide (PI) staining was performed to analyze the cell cycle distribution of Mz-ChA-1 cells and to assess apoptosis by annexin v-fluorescein isothiocyanate (V-FITC)/PI staining. Rh123 staining was used to detect the alteration of mitochondrial membrane potential (ΔΨm). The protein levels of Bax, Bcl-2, Cdk2, cytochrome c and caspase-3 were further confirmed by Western blotting.
RESULTS: ESC-3 significantly inhibited the growth of three human cholangiocarcinoma cell lines and arrested Mz-ChA-1 cell cycle at G0/G1 phase. Mz-ChA-1 cells showed typical apoptotic morphological changes after treated with ESC-3 (10 μg/mL) for 48 h. Cell death assay indicated that Mz-ChA-1 cells underwent apoptosis in a dose-dependent manner induced by ESC-3. In addition, ESC-3 treatment could downregulate the protein level of Bcl-2 and upregulate the Bax, leading to the increase in the ratio of Bax to Bcl-2 in Mz-ChA-1 cells. Meanwhile, cytochrome c was released from the mitochondria into the cytosol, which subsequently initiated the activation of caspase-3. All these events were associated with the collapse of the mitochondrial membrane potential.
CONCLUSION: ESC-3, the active ingredient of crocodile bile, induced apoptosis in Mz-ChA-1 cells through the mitochondria-dependent pathway and may be a potential chemotherapeutic drug for the treatment of cholangiocarcinoma.
PMCID: PMC3281230  PMID: 22363144
Crocodylus siamensis bile; Cholangiocarcinoma; Antiproliferation; Apoptosis; Mitochondria

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