Exogut Formation by the Treatment of Sea Urchin Embryos with Ascorbate and α-Ketoglutarate

In sea urchin embryos at the stages from hatch out to the pluteus stage, [¹⁴C]proline incorporation into hot trichloroacetic acid TCA-extractable proteins occurred during an exposure to [¹⁴C]proline for 3 hrs at 20°C. The rate of [¹⁴C]proline incorporation into hot TCA-extractable proteins was higher in gastrulae and plutei than in blastulae. Percentage of [¹⁴C]hydroxyproline residue to whole radioactivity of the hot TCA-extractable proteins was quite low at the blastula stage and increased exponentially during futher development. Production of [¹⁴C]hydroxyproline residue at the blastula stage, as well as at the later stages, was stimulated by ascorbate and α-ketoglutarate, activators of protocollagen proline hydroxylase, and inhibited by α, α'-dipyridyl, an inhibitor of this enzyme. It is also probable that the enzyme in the embryos is not fully activated because of low amounts of activating substances. These suggest that blastulae,…, also have a potency of protocollagen hydroxylation. Blastula kept in sea water containing ascorbateand α-ketoglutarate became undeveloped embryo with large exogut. Gastrula developed normally to pluteus even in the presence of these compounds. The embryos, kept in sea water containing these compounds from fertilization to hatch out, also developed normally. Exogut formation in the embryos treated by these compounds, as well as normal archenteron formation, was inhibited by α, α'-dipyridyl.     

A method for evaluating the results of Bayesian model selection: application to linkage analyses of attributes determined by two or more genes

OBJECTIVES: We apply and evaluate the intrinsic Bayes factor (IBF) of Berger and Pericchi [J Am Stat Assoc 1996;91:109-122; Bayesian Statistics, Oxford University Press, vol 5, 1996] to linkage analyses done using the stochastic search variable selection (SSVS) method of George and McCulloch [J Am Stat Assoc 1993;88:881-889] as proposed by Suh et al. [Genet Epidemiol 2001;21(suppl 1):S706-S711]. METHODS: We consider 20 simulations of linkage data obtained under two different generating models. The SSVS is applied to a multiple regression extension [Genet Epidemiol 2001;21(suppl 1): S706-S711] of the Haseman-Elston [Behav Genet 1972;2:3-19; Genet Epidemiol 2000;19:1-17] methods. Four prior distributions are considered. We apply the IBF criterion to those samples where different prior distributions result in different top models. RESULTS: In those samples where three different models were obtained using the four priors, application of the IBFs eliminated one of the two wrong models in 4 out of 5 situations. Further elimination using the IBF criterion for situations with two different subsets did not serve as well. CONCLUSIONS: When different priors result in three or more different subsets of markers, one can use the IBF to get this number down to two for consideration. When two subsets result we recommend that both be considered.     

Poly-ADP-ribosylated histones: potent DNA suppressors

When rat liver nuclear chromatin was sonicated in buffer containing 0.35 M (NH₄)SO₄ to release the engaged RNA polymerases, a potent inhibitor was also released. This inhibitor elicited dramatic inhibition of RNA synthesis regardless of whether the free or engaged RNA polymerase was used. On further analysis, it became apparent that the site of inhibition was on the DNA template, not on the enzyme. This inhibitor could be extracted into 0.25 N HCl by the standard procedure for the isolation of histones. This acid-soluble inhibitor, showing typical histone band on gel, was RNase A and DNase I resistant, but was sensitive to both pronase and snake venom phosphodiesterase digestion, as well as to 0.1 N KOH hydrolysis. Furthermore, when [¹⁴C]adenine labeled poly-ADP-ribosylated histones were digested by snake venom phosphodiesterase, the release of radioactivity was in parallel to the loss of inhibitor activity. We conclude that the inhibitor substances are poly-ADP-ribosylated histones and propose that the poly-ADP-ribosylated histones rather than the histones are the natural suppressors of the gene.     

Cross-hybridizing snake satellite, Drosophila, and mouse DNA sequences may have arisen independently

Previous reports have interpreted hybridization between snake satellite DNA and DNA clones from a variety of distant taxonomic groups as evidence for evolutionary conservation, which implies common ancestry (homology) and/or convergence (analogy) to produce the cross- hybridizing sequences. We have isolated 11 clones from a genomic library of Drosophila melanogaster, using a cloned 2.5-kb snake satellite probe of known nucleotide sequence. We have also analysed published sequence data from snakes, mice, and Drosophila. These data show that (1) all of the cross-hybridization between the snake, fly, and mouse clones can be accounted for by the presence of either of two tandem repeats, [GATA]n and [GACA]n and (2) these tandem repeats are organized differently among the different species. We find no evidence that these sequences are homologous apart from the existence of the simple repeat itself, although their divergence from a common ancestral sequence cannot be ruled out. The sequences contain a variety of homogeneous clusters of tandem repeats of CATA, GA, TA, and CA, as well as GATA and GACA. We suggest that these motifs may have arisen by a self-accelerating process involving slipped-strand mispairing of DNA. Homogeneity of the clusters might simply be the result of a rate of accumulation of tandem repeats that exceeds that of other mutations.      

Personal commentaryWho should be reporting gynaecological cytopathology?

If I were Rip van Winkle and woke up after a 30-year-long slumber, I could find much that is new in cervical cancer screening except for one thing. Medically qualified consultant histo/cytopathologists are still expected to look at, and report on, all abnormal smears and biomedical scientists/medical laboratory scientific officers can only play an intermediate role between screeners and consultants. This practice has been cast in stone by expert committees of both the British Society for Clinical Cytology (BSCC) ^1,2 and the Royal College of Pathologists (RCPath) ³ in the following terms: 'All abnormal smears, including those with borderline nuclear changes, should be reported by a cytopathologist …' ¹ and 'The laboratory should be supervised by a consultant cytopathologist and he/she, or deputy, should be in attendance at the laboratory every working day … The cytopathologist should see all abnormal material and a proportion of the negative material …' ² and 'Cervical screening specimens in which abnormal or equivocal cells are present must … be examined by a pathologist …' ³ > (wording unchanged in two subsequent editions).     

Unifying Time to Contact Estimation and Collision Avoidance across Species

The [Formula: see text]-function and the [Formula: see text]-function are phenomenological models that are widely used in the context of timing interceptive actions and collision avoidance, respectively. Both models were previously considered to be unrelated to each other: [Formula: see text] is a decreasing function that provides an estimation of time-to-contact (ttc) in the early phase of an object approach; in contrast, [Formula: see text] has a maximum before ttc. Furthermore, it is not clear how both functions could be implemented at the neuronal level in a biophysically plausible fashion. Here we propose a new framework - the corrected modified Tau function - capable of predicting both [Formula: see text]-type ("[Formula: see text]") and [Formula: see text]-type ("[Formula: see text]") responses. The outstanding property of our new framework is its resilience to noise. We show that [Formula: see text] can be derived from a firing rate equation, and, as [Formula: see text], serves to describe the response curves of collision sensitive neurons. Furthermore, we show that [Formula: see text] predicts the psychophysical performance of subjects determining ttc. Our new framework is thus validated successfully against published and novel experimental data. Within the framework, links between [Formula: see text]-type and [Formula: see text]-type neurons are established. Therefore, it could possibly serve as a model for explaining the co-occurrence of such neurons in the brain.     

PRODUCT OPTIMIZATION AND THE ACCEPTOR SET SIZE

The acceptability of a product, measured by the acceptor set size (percentage of consumers rating the product acceptable), is a function of the perception of its attributes. The attributes are themselves a function of the inputs to the product (such as ingredients, processing or storage variables). These assumptions lead to the following model:
Acceptor set size = F (attribute₁, attribute₂, …, attribute_n)
Attribute j = f (input₁, input₂, …, input_m)
If we assume that these functions are differentiable, we can estimate the partial derivatives of the acceptor set size, with respect to the input variables. The gradient vector obtained indicates the fastest way to maximize the acceptor set size. The gradient search method, using the acceptor set size as an objective measure, can be applied in a variety of situations: to improve existing products, to maximize the acceptability of new products, and to study the relationship between shelf-life and acceptability.     

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNA^Leu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.[Reviewing Editor: Dr. Bill Ballard]     

Structural determinants conferring unusual long life in human serum to rattlesnake‐derived antimicrobial peptide Ctn[15‐34]

Ctn[15‐34], a downsized version of the snake venom cathelicidin‐like peptide crotalicidin (Ctn), shows an unusually high lifespan (t_1/2, approximately 12 h) in human serum, which significantly adds to its promise as an antimicrobial and antitumor agent. Herein we investigate the role of Ctn[15‐34] structure on serum survival. Using a set of analogs, we show that C‐terminal amidation, as well as the specific layout of the Ctn[15‐34] sequence—a helical N‐terminal domain followed by a hydrophobic domain—is crucial for slow degradation, and any change in their arrangement results in significantly lower t_1/2. Aside from the privileged primary structure, features such as self‐aggregation can be ruled out as causes for the long serum life. Instead, studies in other protease‐rich fluids suggest a key role for certain human serum components. Finally, we demonstrate that Ctn[15‐34] is able to induce bacterial death even after 12‐hour pre‐incubation in serum, in agreement with the proteolytic data. Altogether, the results shed light on the uncommon stability of Ctn[15‐34] in human serum and confirm its potential as an anti‐infective lead.     

NAD[S], an NAD analogue with reduced susceptibility to phosphodiesterase. Chemical synthesis and enzymic properties

The chemical synthesis of adenosine(5') [alpha-thio]diphospho(5')ribofuranosyl-nicotinamide (NAD[S]) is described. The product occurs as a pair of diastereomers with different configuration at the sulfur-bearing phosphorus atom. The diastereomers were separated by high-performance liquid chromatography and their absolute configuration was determined after chemical degradation to the ADP[alpha S] diastereomers and chromatographic comparison with enzymically synthesized ADP[alpha S] diastereomers of known absolute configuration. Additional support for this assignment is based on different rates in the phosphodiesterase-catalyzed hydrolysis. Furthermore the synthesis of [14C]NAD[S] is described. The coenzyme activity of NAD[S] in the reaction with alcohol dehydrogenase from baker's yeast and lactate dehydrogenase from pig heart is very similar to that of beta-NAD. Also, NAD and NAD[S] serve equally well as substrates for NAD glycohydrolase from calf spleen. In contrast, no reaction was detected with NAD pyrophosphorylase, and hydrolysis of the separated NAD[S] diastereomers with snake venom phosphodiesterase showed a 26-fold and a 33-fold slower reaction rate than that of NAD. Nucleotide pyrophosphatase was less sensitive to the S substitution, hydrolyzing NAD[S] 14-times slower than NAD. Poly(ADP-ribose) polymerase from Ehrlich ascites tumor cell nuclei accepted NAD[S] as a substrate but the reaction was significantly slower and approached saturation at much lower values than with NAD. Alkaline hydrolysis of the products insoluble in trichloroacetic acid yielded AMP[S] as the main derivative. It is concluded that with NAD[S] as a substrate the nuclear acceptors were nearly exclusively mono(ADP-ribosyl) ated .     

An artificial intelligence model to identify snakes from across the world: Opportunities and challenges for global health and herpetology

BackgroundSnakebite envenoming is a neglected tropical disease that kills an estimated 81,000 to 138,000 people and disables another 400,000 globally every year. The World Health Organization aims to halve this burden by 2030. To achieve this ambitious goal, we need to close the data gap in snake ecology and snakebite epidemiology and give healthcare providers up-to-date knowledge and access to better diagnostic tools. An essential first step is to improve the capacity to identify biting snakes taxonomically. The existence of AI-based identification tools for other animals offers an innovative opportunity to apply machine learning to snake identification and snakebite envenoming, a life-threatening situation.MethodologyWe developed an AI model based on Vision Transformer, a recent neural network architecture, and a comprehensive snake photo dataset of 386,006 training photos covering 198 venomous and 574 non-venomous snake species from 188 countries. We gathered photos from online biodiversity platforms (iNaturalist and HerpMapper) and a photo-sharing site (Flickr).Principal findingsThe model macro-averaged F1 score, which reflects the species-wise performance as averaging performance for each species, is 92.2%. The accuracy on a species and genus level is 96.0% and 99.0%, respectively. The average accuracy per country is 94.2%. The model accurately classifies selected venomous and non-venomous lookalike species from Southeast Asia and sub-Saharan Africa.ConclusionsTo our knowledge, this model’s taxonomic and geographic coverage and performance are unprecedented. This model could provide high-speed and low-cost snake identification to support snakebite victims and healthcare providers in low-resource settings, as well as zoologists, conservationists, and nature lovers from across the world.     

Host shift by the burying beetle, Nicrophorus pustulatus, a parasitoid of snake eggs

Recent work [Ecoscience (2000) vol. 7, 395-397] suggests that the burying beetle Nicrophorus pustulatus may have undergone a remarkable host shift, exploiting snake eggs rather than carrion as resources for breeding. We conducted behavioural and physiological experiments to examine the hypothesis of a host shift and to formulate hypotheses on its origin. Two congeners of N. pustulatus, Nicrophorus orbicollis and Nicrophorus defodiens did not respond to snake eggs with typical breeding behaviour. When N. pustulatus male-female pairs (n = 14) were presented with clutches of snake eggs, the number of offspring but not the mean size of offspring varied with snake egg mass, indicating effective regulation of brood size. When breeding on turtle eggs, N. pustulatus had a more variable response than when exploiting snake eggs, suggesting that turtle eggs are not a primary resource for breeding. Nicrophorus pustulatus presented with both snake eggs and a mouse carcass combined and exploited the two resources within the same nest (10 of 12 trials). Mouse carcasses and snake eggs were treated differently. Carcasses were moved, buried and stripped of hair in a manner characteristic of burying beetles, whereas snake eggs were not moved or buried. Females that discovered a mouse carcass also had a significantly greater juvenile hormone increase than did females discovering snake eggs. Some responses to the two resources, however, were similar. Female N. pustulatus oviposited rapidly in response to either a mouse carcass or snake eggs, and males elevated sex pheromone emission in response to either resource. The efficient use of snake eggs, the ability to regulate brood size and the different responses to snake eggs and carrion suggest that N. pustulatus is well adapted to exploiting snake eggs for breeding. The use of snake eggs by N. pustulatus has potential implications for conservation of oviparous reptiles.     

Stereochemistry of hydrolysis by snake venom phosphodiesterase.

[18O]Adenosine 5'-O-phosphorothioate-O-p-nitrophenyl ester was prepared by saponification of the bis (-O,O-p-nitrophenyl ester) with K18OH. Only the diastereoisomer with the Rp configuration si a substrate for snake venom phosphodiesterase. The asymmetrically labeled [18O]adenosine 5'-O-phosphorothioate formed in this reaction was converted enzymatically to [18O]adenosine 5'-(1-thiodiphosphate) with the Sp configuration. The position of the 18O label, either bridging [1,2-mu-18O] or nonbridging [1-18O] was then determined. The results show that the reaction catalyzed by snake venom phosphodiesterase takes place with retention of configuration at phosphorus. This indicates that the hydrolysis proceeds via a covalent nucleotide enzyme intermediate.     

Distribution of sea snakes in the Great Barrier Reef Marine Park: observations from 10 yrs of baited remote underwater video station (BRUVS) sampling

The distributions of three species of sea snake (olive sea snake: Aipysurus laevis, spine-bellied sea snake: Lapemis curtus, and ornate sea snake: Hydrophis ocellatus) were estimated over 14° of latitude within the Great Barrier Reef Marine Park (GBRMP) using data from baited remote underwater video stations (BRUVS). A total of 2,471 deployments of BRUVS were made in a range of locations, in sites open and closed to trawl fishing. Sightings of sea snakes were analysed alongside six spatial factors [depth, relative distance across (longitude) and along (latitude) the GBRMP, proximity to land, proximity to the nearest reef, and habitat complexity] to determine the factors that most strongly influenced the distribution and abundance of sea snakes. The results showed a strong latitudinal effect on the distribution of all three sea snake species, with the highest densities and diversities occurring in central and southern GBRMP locations, while the northern Great Barrier Reef was relatively depauperate in terms of both occurrence and diversity. Shallow inshore areas were identified as key habitats for A. laevis and L. curtus, whereas deeper offshore habitats were most important for H. ocellatus. No significant difference was found in the mean number of snakes sighted per hour between sites open and closed to trawling. There was a high degree of congruence in the distribution of sea snakes estimated from the BRUVS data and results from previous trawl and underwater visual surveys, demonstrating the utility of BRUVS to estimate distribution and relative abundance in these species of sea snake at broad spatial scales in a non-extractive manner.     

Snake venom as therapeutic agents: from toxin to drug development

Snake bite injuries and death are socio-medical problems of considerable magnitude. In India a large number of people suffer and die every year due to snake venom poisoning. Snake venom, though greatly feared, is a natural biological resource, containing several components that could be of potential therapeutic value. Use of snake venom in different pathophysiological conditions has been mentioned in Ayurveda, homeopathy and folk medicine. It is well known that snake venom is complex mixture of enzymes, peptides and proteins of low molecular mass with specific chemical and biological activities. Snake venom contains several neurotoxic, cardiotoxic, cytotoxic, nerve growth factor, lectins, disintrigrins, haemorrhagins and many other different enzymes. These proteins not only inflict death to animals and humans, but can also be used for the treatment of thrombosis, arthritis, cancer and many other diseases. An overview of various snake venom components that have prospects in health and diseases are discussed in this review.     

Synthesis and enzymatic characterization of P1-thio-P2-oxo trideoxynucleoside diphosphates having AZT, FdU, or dT at the 3'-position

Model compounds for oligonucleotide-prodrugs, P1-thio-P2-oxo-trideoxyribonucleoside diphosphates: d[G(s)C(o)X] and d[T(s)A(o)X] (X = AZT, FdU or dT) have been prepared, and their hydrolyses by snake venom phosphodiesterase and nuclease S1 are described.     

Of Clues and Signs: The Dead Body and Its Evidential Traces

ABSTRACT   Taking the conflict over the remains of Ned Kelly as a starting point, in this article I trace the various conceptions of the, body as evidence within the intertwined histories of anthropology, criminology, and medicine to explore how anthropological practice brings the dead into being through exhumation and analysis. I outline the popular rhetorical tropes within which evidentiary claims are situated, exploring how the agency of people after death is understood within the framework of present-day forensic anthropological practice and how this is underwritten by a particular heritage of anatomical analysis. [Keywords: archaeology, forensic anthropology, materiality, semiotics of the body]     

Amino acid-specific ADP-ribosylation

[adenine-U-14C]ADP-ribose-agmatine and [adenine-U-14C ))ADP-ribose-histone were synthesized by an NAD:arginine ADP-ribosyltransferase from [14C]NAD and agmatine and histone, respectively. The pseudo-first order rate constants for breakdown of the two components either in 0.4 N NaOH or in 0.4 M neutral hydroxylamine were identical. Hydroxylamine treatment of [14C]ADP-ribose-agmatine or [32P]ADP-ribose-histone yielded a single radioactive product which was separated by high pressure liquid chromatography and identified as ADP-ribose-hydroxamate by the formation of a ferric chloride complex. Hydrolysis of ADP-ribose-hydroxamate with snake venom phosphodiesterase resulted in the formation of 5'-AMP, consistent with the presence of a pyrophosphate bond. Incubation of ADP-ribose-[14C]agmatine, synthesized by the ADP-ribosyltransferase from NAD and [14C]agmatine, with 0.4 M neutral hydroxylamine resulted in the release of [14C]agmatine rather than phosphoribosyl[14C]agmatine. In addition, neither NAD nor ADP-ribose reacts with hydroxylamine; i.e. there was no evidence of nucleophilic attack by hydroxylamine at the pyrophosphate bond. The ADP-ribosyl-protein linkage formed by the NAD:arginine ADP-ribosyltransferase is considerably more stable to hydroxylamine than is the ADP-ribose-glutamate bond. The presence of ADP-ribose-arginine and ADP-ribose-glutamate synthesized by the ADP-ribosyltransferase and poly(ADP-ribose) synthetase, respectively, may be the chemical basis for the "hydroxylamine-stable" and "hydroxylamine-labile" bonds described by Hilz (Hilz, H. (1981) Hoppe-Seyler's Z. Physiol. Chem. 362, 1415-1425).     

Lipolytic enzymes in bovine thyroid tissue. I. Subcellular localization, purification and characterization of acid phospholipase A1.

In mammalian cells the catabolism of membrane phosphoglycerides proceeds probably entirely through a deacylation pathway catalysed by phospholipase A and lysophospholipase (Wise & Elwyn, 1965). In the initial attack of diacylphosphoglycerides by phospholipase A two enzymatic activities with different positional specificities have been distinguished: phospholipase A1 (phosphatidate 1-acyl hydrolase EN 3.1.1.32) and phospholipase A2 (phosphatidate 2-acyl hydrolase EN 3.1.1.4) (Van Deenen & De Haas, 1966). Studies on these intracellular phospholipases were mainly concerned with their subcellular localization. Only occasionally more detailed enzymatic investigations have been conducted on them, in contrast to export phospholipases e.g. from snake venom, bee venom and porcine pancreas, which have been extensively investigated (Brockerhoff & Jensen 1974a). In a previous paper (De Wolf et al., 1976a), the presence of phospholipase A1 and phospholipase A2 activities in bovine thyroid was demonstrated, using 1-[9, 10-3H] stearoyl-2-[1-14C] linoleyl-sn-glycero-3-phosphocholine as a substrate. Optimal activity was observed in both instances at pH 4. Addition of the anionic detergent sodium taurocholate increased the A2 type activity and decreased the A1 type activity suggesting the presence of different enzymes. The lack of influence of Ca2+-ions and EDTA and the acid pH optima could suggest lysosomal localization. In this paper the subcellular distribution of both acid phospholipase activities is described as well as a purification scheme for phospholipase A1. Some characteristics of the purified enzyme preparation are discussed.