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PubMed2002

PHENIX: building new software for automated crystallographic structure determination.

Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.

Algorithms↗

PubMed2004

Untangle, a tool for filtering overlapping diffraction patterns from multicrystals.

Standard crystallographic data-processing protocols are based on single-crystal models; data from aggregates of multiple crystals with different orientations are difficult to process. In certain cases, it is possible to separately index the diffraction patterns from the dominant crystals in the aggregate. Untangle is a program designed to identify and eliminate overlapping spots from such patterns in order to improve data quality. The program has a Python core with a simple and highly portable graphical user interface, permitting visual verification of the process and interactive modification of the overlap threshold. The software is available under an open-source license.

Bacterial Proteins↗

PubMed2001

IFEFFIT: interactive XAFS analysis and FEFF fitting.

IFEFFIT, an interactive program and scriptable library of XAFS algorithms is presented. The core algorithms of AUTOBK and FEFFIT have been combined with general data manipulation and interactive graphics into a single package. IFEFFIT comes with a command-line program that can be run either interactively or in batch-mode. It also provides a library of functions that can be used easily from C or Fortran, as well as high level scripting languages such as Tcl, Perl and Python. Using this library, a Graphical User Interface for rapid 'online' data analysis is demonstrated. IFEFFIT is freely available with an Open Source license. Outside use, development, and contributions are encouraged.

Journal Article↗

PubMed2003

Recent developments in the PHENIX software for automated crystallographic structure determination.

A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed for the automation of crystallographic structure solution. This will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described.

Algorithms↗

PubMed1990

Shed snake skin and hairless mouse skin as model membranes for human skin during permeation studies.

Difficulties in obtaining and using human skin have tempted many workers to employ animal membranes for percutaneous absorption studies. We have investigated the suitability of two species of snake (Elaphe obsoleta, Python molurus) for this purpose and compared our in vitro experimental results for human skin and for hairless mouse, a currently popular model. The effects of long-term hydration on the membranes were investigated over 8 d using tritiated water as a model permeant. The initial permeability coefficients of all the membranes were similar (0.74-2.2 X 10(-3) cm 2h-1). Although the human and squamate skins did not change significantly over the test period, the permeability of hairless mouse skin increased 37 times. The actions of typical enhancers on the permeabilities of the membranes to a model penetrant 5-fluorouracil (5-FU) were tested using 3% Azone in Tween 20/saline, propylene glycol (PG), 2% Azone in PG, and 5% oleic acid in PG. While the data from snake membranes tended to underestimate the enhancer effects, those from hairless mouse skin greatly overestimated the changes. None of the membranes was a completely reliable model for assessing human percutaneous absorption as modified by accelerants. Pretreatment with acetone did not significantly change the permeability of human or squamate skins to 5-FU, although that of hairless mouse increased twentyfold. An overall conclusion is that, wherever possible, human skin should be used in absorption studies and not hairless mouse or snake skin; otherwise, misleading results may be obtained.

Acetone↗

PubMed1975

Human infestation by Ophionyssus natricis snake mite.

A family presented with a papular vesiculo-bullous eruption of the skin, found to be caused by the snake mite, Ophionyssus natricis (Cervais, 1844). A pet python was the primary host. Treatment of the animal and its environment led to clearance of the human skin lesions.

Adult↗

PubMedDate not supplied

Cross reactivity between venomous, mildly venomous, and non-venomous snake venoms with the Commonwealth Serum Laboratories Venom Detection Kit.

OBJECTIVE: Studies have noted the relatively common occurrence of positive urine results with the Commonwealth Serum Laboratories Venom Detection Kit (VDK) when testing patients with suspected snakebite who are not envenomed. Possible explanations have been false positive test results or subclinical envenoming. We investigated a third possibility, that there is potential for the venom (or saliva) from mildly venomous and non-venomous snakes to give a positive reading with the VDK. METHODS: Venoms/saliva from three non-venomous and seven mildly venomous snake species were tested in the laboratory with the VDK, along with control venoms from four of the five major snake genera (Brown snake, Tiger snake, Death adder and Black snake). RESULTS: Two of the venom/saliva samples, from Gould's hooded snake (Parasuta gouldii), a mildly venomous snake, and the Black-headed python (Aspidites melanocephalus), a non-venomous snake, caused a positive test for the tiger snake genus. There was also cross-reactivity between black snake venoms and the tiger snake well of the VDK. CONCLUSIONS: This study provides a further possible explanation for 'false positive' VDK results, that is venom/saliva presence or absorption from mildly or non-venomous snakes and cross reactivity with venomous snakes on VDK testing. It has implications for antivenom use should it ever be required for more severe envenoming syndromes from mildly or moderately venomous snakes, and for further research. It reinforces the practice of only using VDK testing in patients who show definite evidence of envenoming.

Animals↗

PubMed2000

A fossil snake with limbs.

A 95-million-year-old fossil snake from the Middle East documents the most extreme hindlimb development of any known member of that group, as it preserves the tibia, fibula, tarsals, metatarsals, and phalanges. It is more complete than Pachyrhachis, a second fossil snake with hindlimbs that was recently portrayed to be basal to all other snakes. Phylogenetic analysis of the relationships of the new taxon, as well as reanalysis of Pachyrhachis, shows both to be related to macrostomatans, a group that includes relatively advanced snakes such as pythons, boas, and colubroids to the exclusion of more primitive snakes such as blindsnakes and pipesnakes.

Animals↗

PubMed1980

Monkey responses to three different alarm calls: evidence of predator classification and semantic communication.

Vervet monkeys give different alarm calls to different predators. Recordings of the alarms played back when predators were absent caused the monkeys to run into trees for leopard alarms, look up for eagle alarms, and look down for snake alarms. Adults call primarily to leopards, martial eagles, and pythons, but infants give leopard alarms to various mammals, eagle alarms to many birds, and snake alarms to various snakelike objects. Predator classification improves with age and experience.

Animal Communication↗

PubMed2006

Dissociation of a MAVS/IPS-1/VISA/Cardif-IKKepsilon molecular complex from the mitochondrial outer membrane by hepatitis C virus NS3-4A proteolytic cleavage.

Intracellular RNA virus infection is detected by the cytoplasmic RNA helicase RIG-I that plays an essential role in signaling to the host antiviral response. Recently, the adapter molecule that links RIG-I sensing of incoming viral RNA to downstream signaling and gene activation events was characterized by four different groups; MAVS/IPS-1-1/VISA/Cardif contains an amino-terminal CARD domain and a carboxyl-terminal mitochondrial transmembrane sequence that localizes to the mitochondrial membrane. Furthermore, the hepatitis C virus NS3-4A protease complex specifically targets MAVS/IPS-1/VISA/Cardif for cleavage as part of its immune evasion strategy. With a novel search program written in python, we also identified an uncharacterized protein, KIAA1271 (K1271), containing a single CARD-like domain at the N terminus and a Leu-Val-rich C terminus that is identical to that of MAVS/IPS-1/VISA/Cardif. Using a combination of biochemical analysis, subcellular fractionation, and confocal microscopy, we now demonstrate that NS3-4A cleavage of MAVS/IPS-1/VISA/Cardif/K1271 results in its dissociation from the mitochondrial membrane and disrupts signaling to the antiviral immune response. Furthermore, virus-induced IKKepsilon kinase, but not TBK1, colocalized strongly with MAVS at the mitochondrial membrane, and the localization of both molecules was disrupted by NS3-4A expression. Mutation of the critical cysteine 508 to alanine was sufficient to maintain mitochondrial localization of MAVS/IPS-1/VISA/Cardif and IKKepsilon in the presence of NS3-4A. These observations provide an outline of the mechanism by which hepatitis C virus evades the interferon antiviral response.

Adaptor Proteins, Signal Transducing↗

PubMed2000

The Ensemble/Legacy Chimera extension: standardized user and programmer interface to molecular Ensemble data and Legacy modeling programs.

Ensemble/Legacy is a toolkit extension of the Object Technology Framework (OTF) that exposes an object oriented interface for accessing and manipulating ensembles (collections of molecular conformations that share a common chemical topology) and driving Legacy programs (such as MSMS, AMBER, X-PLOR, CORMA/MARDIGRAS, Dials and Windows, and CURVES). Ensemble/Legacy provides a natural programming interface for running Legacy programs on ensembles of molecules and accessing the resulting data. Using the OTF reduces the time cost of developing a new library to store and manipulate molecular data and also allows Ensemble/Legacy to integrate into the Chimera visualization program. The extension to Chimera exposes the Legacy functionality using a graphical user interface that greatly simplifies the process of modeling and analyzing conformational ensembles. Furthermore, all the C++ functionality of the Ensemble/Legacy toolkit is "wrapped" for use in the Python programming language. More detailed documentation on using Ensemble/Legacy is available online (http:¿picasso.nmr.ucsf.edu/dek/ensemble. html).

Computer Graphics↗

PubMed1980

Dorsal root projections in various types of reptiles.

The distribution of dorsal root fibers into the spinal cord as well as to the brainstem have been studied in various types of reptiles. At the site of entrance into the spinal cord no clear segregation of large fibers medially and smaller fibers laterally has been observed. A peculiarity for reptiles seems to be a lateral bundle of primary afferent fibers which traverses the dorsal part of the lateral funiculus. The fibers of this bundle enter the spinal gray at the lateral side of the dorsal horn. Notable variation in the distribution of dorsal root fibers has been observed in the reptiles studied. In the turtle Testudo hermanni and in the snake Python reticulatus almost no fibers were found to extend into the ventral horn. However, in the lizard Tupinambis nigropunctatus a distinct projection into the ventral horn was observed. This closer potential coupling between the primary input and output systems of the spinal cord than in the turtle Testudo hermanni seems to be related to the long multijointed digits in the lizard studied which give its limbs a marked prehensile character.

Afferent Pathways↗

PubMed1987

A comparative study on glyoxalase II from vertebrata.

S-2-hydroxyacylglutathione hydrolase (glyoxalase II) from the liver of animals belonging to the various vertebrate classes (Oryctolagus cuniculus, Gallus gallus, Python molurus, Rana esculenta, Esox lucius) have been purified from 100,000 g supernatants of liver homogenates, using acetone fractionation and affinity chromatography. Subsequent comparative studies were concerned with some molecular and kinetic properties. Isoelectric focusing gave evidence for a single form of liver glyoxalase II in O. cuniculus, P. molurus and E. lucius, while the enzyme from G. gallus and R. esculenta showed respectively two and three forms with different pI values. All studied enzymes are basic proteins. The relative molecular mass values range from 18,000 to 23,000. The various glyoxalases II do not display markedly different Kn or Ki values. Their stability behavior at different temperatures is also quite similar.

Animals↗

PubMed1985

Localization of immunoreactive synthetic atrial natriuretic factor (ANF) in the heart of various animal species.

The localization of two synthetic fragments of the C-terminal portion of atrial natriuretic factor: Arg 101-Tyr 126 which displays full biological activity and Leu 94-Arg 109 which is completely devoid of biological activity, has been investigated by immunohisto- and immunocytochemical methods in the heart of mammals (rat, mouse, guinea pig, hamster, rabbit, cat, dog, man) and nonmammalian vertebrates toad (Bufo marinus), frog (Rana catesbeiana), fish (Cyprinus carpio, Puntius schwanenfeldi, Cichlosoma biocellatum, Carrasius auratus), snake (Python reticulatus) and hen. Antibodies against the synthetic fragments of ANF were raised in rabbits and used either for immunofluorescence (Coons' technique), immunohistochemistry (unlabeled antibody technique) or immunocytochemistry (protein A-gold technique). Results obtained by immunofluorescence and by the unlabeled antibody technique were similar: antibodies against Arg 101-Tyr 126 ANF allowed visualization of granulated cardiocytes in the atria of all mammals. While the reaction was very strong in rat and mouse, it was less so in the rabbit and very weak in all other species studied including man. Antibodies against Leu 94-Arg 109 ANF produced a reaction only in the rat and mouse. In nonmammalian vertebrates, the reaction was always much stronger in atria than ventricles of all species with both antibodies.

Animals↗

PubMed2004

PyEvolve: a toolkit for statistical modelling of molecular evolution.

BACKGROUND: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. RESULTS: Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. CONCLUSION: PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Animals↗

PubMed2005

Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.

BACKGROUND: Various forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an N- and a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when implementing local moves for Markov Chain Monte Carlo simulations. Most loop closure algorithms keep the bond angles fixed or semi-fixed, and only vary the dihedral angles. This is appropriate for a full-atom protein backbone, since the bond angles can be considered as fixed, while the (phi, psi) dihedral angles are variable. However, many de novo structure prediction methods use protein models that only consist of Calpha atoms, or otherwise do not make use of all backbone atoms. These methods require a method that alters both bond and dihedral angles, since the pseudo bond angle between three consecutive Calpha atoms also varies considerably. RESULTS: Here we present a method that solves the loop closure problem for Calpha only protein models. We developed a variant of Cyclic Coordinate Descent (CCD), an inverse kinematics method from the field of robotics, which was recently applied to the loop closure problem. Since the method alters both bond and dihedral angles, which is equivalent to applying a full rotation matrix, we call our method Full CCD (FCDD). FCCD replaces CCD's vector-based optimization of a rotation around an axis with a singular value decomposition-based optimization of a general rotation matrix. The method is easy to implement and numerically stable. CONCLUSION: We tested the method's performance on sets of random protein Calpha segments between 5 and 30 amino acids long, and a number of loops of length 4, 8 and 12. FCCD is fast, has a high success rate and readily generates conformations close to those of real loops. The presence of constraints on the angles only has a small effect on the performance. A reference implementation of FCCD in Python is available as supplementary information.

Algorithms↗

PubMed2004

Some methods for blindfolded record linkage.

BACKGROUND: The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects - a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. METHODS: A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. RESULTS: The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. CONCLUSION: Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy.

Computer Communication Networks↗

PubMed2026

Comprehensive in silico genomics analysis of global trends and host-specific emergence of aminoglycoside resistance in Staphylococcus aureus: a One-Health perspective.

BACKGROUND: Aminoglycosides remain clinically valuable against Staphylococcus aureus. Aminoglycoside resistance in S. aureus represents a critical One Health concern and is primarily driven by aminoglycoside-modifying enzymes (AMEs), which are frequently plasmid-encoded. Although regional studies have provided valuable insights, the global epidemiology of aminoglycoside resistance determinants remains poorly characterized because comprehensive data integrating human, animal, and environmental reservoirs are still lacking. This study addresses this gap by analyzing over 110,000 S. aureus genomes (2000-2025) to map the global resistome, quantify temporal and host-specific trends, and assess the association between genetic determinants and phenotypic resistance. METHODS: We performed a retrospective One Health meta-analysis of 110,309 S. aureus genomes collected between 2000 and 2025 from 128 countries. Genomes were quality-filtered and aminoglycoside resistance determinants were identified using NCBI AMRFinderPlus (v4.0.23). Multilocus sequence typing and host-source harmonization (Human, Animal, Environment, Unknown) enabled clonal and reservoir stratification. Temporal trends in gene prevalence and resistance burden were modeled with robust regression. Geographic and host-associated structuring of key genes was assessed via χ2 and enrichment tests. Machine-learning models (elastic-net, random forests, XGBoost) were benchmarked for minimum inhibitory concentration (MIC) prediction via nested cross-validation, with performance evaluated by mean absolute error, RMSE, and SHAP-based feature importance. All analyses were conducted in R and Python using publicly available, de-identified genomic data. RESULTS: Aminoglycoside resistance-associated genes were dominated by modifying enzyme determinants, with ant(6)-Ia, ant(9)-Ia, aph(3')-IIIa, sat4, aadD1, and aac(6')-Ie/aph(2'')-Ia occurring in 14-22% of isolates worldwide. Temporal analysis revealed significant declines in several major determinants, most notably ant(9)-Ia (-2.22 percentage points per year, p < 0.001), whereas apmA exhibited a non-significant decreasing trend in animal isolates. Host structuring was marked: human clinical isolates concentrated common determinants, while animal and environmental isolates harbored rare alleles (apmA, spw, str, spd). Geographic mapping confirmed near-universal distribution of common genes but focal restriction of rare ones. Publicly available phenotypic data indicated strong activity of amikacin, whereas gentamicin showed a distinct resistant subpopulation that closely corresponded with AME gene carriage. Genotype-phenotype analyses demonstrated strong concordance, with gene-rich complements predicting resistant MIC strata and absence of determinants predicting susceptibility. Analysis across different gene classes revealed frequent co-occurrence of aminoglycoside resistance genes with determinants from other classes, such as mecA, blaZ, and MLS_B, embedding them within multidrug-resistant (MDR) genomic contexts. CONCLUSION: Over 25 years, the prevalence of aminoglycoside resistance-associated genes in S. aureus has declined for several common determinants, while rare veterinary-linked alleles are emerging in animal isolates. Strong genotype-phenotype concordance supports genomic prediction for gentamicin and amikacin, where MIC data are available, although phenotypic confirmation remains essential. The frequent co-occurrence of aminoglycoside resistance genes with other antimicrobial resistance determinants indicates their integration within co-occurrence patterns of MDR genes, defined here as clusters of co-occurring resistance genes often carried on shared mobile genetic elements. These patterns highlight the need for integrated One Health surveillance combining clinical, veterinary, and environmental monitoring with plasmid-context resolution to anticipate emerging threats.

Aminoglycosides↗