Decoding hepatorenal tyrosinemia type 1: Unraveling the impact of early detection, NTBC, and the role of liver transplantation

Hepatorenal tyrosinemia type 1 (HT-1) is a rare autosomal recessive disease that results from a deficiency of fumaryl acetoacetate hydrolase (FAH), a critical enzyme in the catabolic pathway for tyrosine. This leads to the accumulation of toxic metabolites such as fumaryl and maleylacetoacetate, which can damage the liver, kidneys, and nervous system. The discovery of 2-[2-nitro-4-trifluoromethylbenzoyl]-1,3-cyclohexanedione (NTBC or nitisinone) has significantly improved the management of HT-1, particularly when initiated before the onset of symptoms. Therefore, newborn screening for HT-1 is essential for timely diagnosis and prompt treatment. The analysis of succinyl acetone (SA) in dried blood spots of newborns followed by quantification of SA in blood or urine for high-risk neonates has excellent sensitivity and specificity for the diagnosis of HT-1. NTBC combined with dietary therapy, if initiated early, can provide liver transplant (LT) free survival and reduce the risk of hepatocellular carcinoma (HCC). Patients failing medical treatment (eg, due to non-adherence), and who develop acute liver failure (ALF), have HCC or evidence of histologically proven dysplastic liver nodule(s), or experience poor quality of life secondary to severe dietary restrictions are currently indicated for LT. Children with HT-1 require frequent monitoring of liver and renal function to assess disease progression and treatment compliance. They are also at risk of long-term neurocognitive impairment, which highlights the need for neurocognitive assessment and therapy.

Visceral Fat Indices: Do They Help Differentiate Crohn's Disease and Intestinal Tuberculosis in Children?

BACKGROUND AND AIMS

Crohn's disease [CD] and intestinal tuberculosis [ITB] are often difficult to differentiate. Mesenteric fat hypertrophy is a feature of CD. We evaluated the utility of fat indices (visceral fat [VF] and subcutaneous fat [SF]) in differentiating CD and ITB in children.

METHODS

Symptomatic children diagnosed to have CD or ITB based on recommended criteria were enrolled. Clinical, anthropometric, and laboratory details were noted. Abdominal fat was measured on computed tomography in supine position at the level of L4 vertebrae. VF and SF area was measured separately by a radiologist, blinded to the diagnosis. The sum of VF and SF was taken as total fat [TF]. VF/SF and VF/TF ratios were calculated.

RESULTS

Thirty-four (age 14 years [10.8-17.0], 14 boys) children were recruited: 12 had CD [seven boys, age 13.0 years] and 22 had ITB [seven boys, age 14.5 years]. VF area was higher in CD compared to ITB (18.34 cm2 [15.62-40.01] vs 6.48 cm2 [2.65-21.96]; p = 0.012). The SF and TF area was similar in ITB and CD. The ratios of VF/SF (0.82 [0.57-1.5] vs 0.33 [0.16-0.48]; p = 0.004) and VF/TF (0.45 [0.36-0.60] vs 0.25 [0.13-0.32]; p = 0.004) were significantly higher in CD. On comparing CD and ITB in boys and girls separately, the difference was significant for boys but not for girls. A VF/SF ratio of 0.609 predicted CD with a good sensitivity [75%] and specificity [86.4%] [area under the curve 0.795, 95% confidence interval 0.636-0.955; p = 0.005].

CONCLUSION

The VF/SF ratio is a simple, non-invasive, objective parameter to differentiate CD and ITB in children, particularly boys. Larger studies are needed to validate this in girls.

A65 VISCERAL FAT INDICES: DO THEY HELP DIFFERENTIATE CROHN’S DISEASE AND INTESTINAL TUBERCULOSIS IN CHILDREN?

Background

Crohn’s disease (CD) and Intestinal tuberculosis (ITB) mimic each other and are often difficult to differentiate. A correct and prompt diagnosis is essential for a good outcome. Mesenteric fat hypertrophy is a feature of CD and studies in adults have shown higher visceral fat in CD than ITB. There is no published data in children.

Purpose

This study evaluated the utility of visceral fat indices in differentiating CD and ITB in children.

Method

Symptomatic children diagnosed to have CD or ITB based on standard recommended criteria were enrolled. The clinical and laboratory details were noted. Abdominal fat was measured on Computed Tomography in supine position at the level of L4 vertebrae. Visceral fat (VF) and subcutaneous fat (SF) area was measured separately by an experienced radiologist, blinded to the diagnosis. Sum of VF and SF was taken as total fat (TF). VF/SF and VF/TF ratio was calculated.

Result(s)

34 children [14 boys, median age 14.0 (inter quartile range 10.8-17.0)] years were recruited, of which 12 (29%) had CD [7 boys, age 13.0 (IQR 9.25-16.5) years] and 22 (71%) had ITB [7 boys, age-14.5 (IQR 11-17) years]. Visceral fat area (VF) was significantly higher in CD compared to ITB (table 1). However, there was no significant difference in the SF (2199.5 (1537.6-3881.6) vs 2176.5 (671.0-6651.5) mm²; p=0.958) and TF (3096.1 (2108.2-5373.5) vs 4518.2 (2677.6-8456.3) mm²; p=0.245) in ITB and CD respectively. The ratio of VF/SF and VF/TF was significantly higher in CD as compared to ITB for all cases (table1). When comparing CD and ITB in boys and girls separately the same trend was observed but the difference was statistically significant only for boys. On ROC analysis, VF:SF ratio of 0.609 predicted CD with the sensitivity of 75% and specificity of 86.4% (area under curve [AUC]-0.795, 95% CI 0.636-0.955; p=0.005). VF:TF ratio of 0.379 had similar sensitivity of 75% and specificity of 86.4% (AUC-0.795, 95% CI 0.636-0.955; p=0.005). The VF area of 1485.26 mm² had a sensitivity of 83.3% and specificity of 72.7% for CD (AUC-0.758, 95% CI 0.590-0.925; p=0.01).

Image

Conclusion(s)

The VF/SF ratio is a simple, non-invasive, objective parameter to differentiate CD and ITB in children with a good sensitivity and specificity.

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Efficacy of amitriptyline in pediatric functional abdominal pain disorders: A randomized placebo-controlled trial

BACKGROUND AND AIM

Amitriptyline improves symptoms in functional abdominal pain disorders (FAPD) in adults with variable results in pediatric studies. The study aims to evaluate the efficacy of amitriptyline in pediatric FAPD.

METHODS

In this open-label trial, children (≤ 18 years) diagnosed as FAPD based on ROME IV criteria were randomized to amitriptyline or placebo for 12 weeks. Post-treatment improvement of pain and quality of life (QOL) from the baseline were compared between the two groups.

RESULTS

The mean age of 149 children (amitriptyline 75, placebo 74) was 11.3 ± 3.5 years (79 boys). There was a significant difference in pain improvement in terms of reduction in scores for intensity (3.4 vs 0.9), frequency (3.6 vs 0.6), duration (3.5 vs 0.9), and QOL (2.3 vs 0.9) between amitriptyline and placebo group (P < 0.001 in all). Responders (> 50% reduction) in pain was seen in 76% in amitriptyline compared with 14.9% in the placebo group (P < 0.001). On multivariate analysis, the use of amitriptyline was the only factor predictive of response (odds ratio 24.1, 95% confidence interval: 9.1-64.6, P < 0.001). Minor adverse events were comparable between the groups (25.3% vs 13.5%, respectively, P = 0.07). Eighty-nine percent of children (24/27) who had extended treatment duration (6.8 ± 1.8 months) had pain improvement. After discontinuation of amitriptyline, 70% had sustained response over a mean follow up of 15.84 ± 5.6 months.

CONCLUSIONS

A 3-month trial of amitriptyline gives sustained relief of pain in two-thirds of children with FAPD. The safety profile of the drug and its efficacy necessitate more frequent use in the clinical settings.

Gastrointestinal bleeding due to pseudoaneurysms in children

Radiological embolization is the treatment of choice in adults with visceral artery pseudoaneurysm (PSA) and gastrointestinal bleeding, but pediatric data is scanty. We analyzed the etiology, clinical presentation, and outcome of radiological intervention in children with PSA of celiac (CA) or superior mesenteric artery (SMA) branches. Electronic records of children with PSA of CA or SMA branches were reviewed and data on clinical and laboratory profile, radiological intervention, and outcome was recorded. Eleven children with PSA (5 boys, 11 [7-17] years) were studied. Etiology was liver abscess (n 4), abdominal trauma (n 3), pancreatitis (n 3), and indeterminate in 1 case. Ten (91%) patients were symptomatic: abdominal pain (10, 91%), hematemesis/melena (9, 81%), and Quincke's triad (1, 9%). One child with pancreatic pseudocyst was diagnosed incidentally on imaging. Doppler ultrasound identified PSA only in 3 cases, while computed tomography angiography (CTA) picked all cases. Children with liver abscess, trauma, and unknown etiology had PSA from CA (right hepatic artery 7, left hepatic artery 1). Of the 3 pancreatitis cases, 2 had PSA from SMA (inferior pancreatico-duodenal artery and ileal branch) and 1 from CA (left gastric artery). Radiological embolization was done in 9 (81%) cases (coil 6, glue 2, both 1), without any complications or failure. One case resolved spontaneously and 1 died pre-intervention. Nine intervened cases were asymptomatic in follow-up [6 (1-24) months].Conclusion: Liver abscess, trauma, and pancreatitis are causes of PSA of CA and SMA branches in children. A majority present with gastrointestinal bleeding and are identified on CTA. Radiological embolization was safe with 100% success. What is Known: • Pseudoaneurysm of visceral artery is an uncommon cause of gastrointestinal bleeding. • Endoluminal intervention is an established and efficacious treatment modality in adults and preferred over surgery. What is New: • Liver abscess, abdominal trauma and pancreatitis are common causes of celiac artery and superior mesenteric artery branch pseudoaneurysm in children and computed tomography angiography has high sensitivity in identifying these pseudoaneurysms. • Minimally invasive radiological angio-embolization, in the hands of trained radiologists, is a safe and successful modality of treatment in children.

Chelation therapy in liver diseases of childhood: Current status and response

Chelation is the mainstay of therapy in certain pediatric liver diseases. Copper and iron related disorders require chelation. Wilson’s disease (WD), one of the common causes of cirrhosis in children is treated primarily with copper chelating agents like D-penicillamine and trientine. D-Penicillamine though widely used due its high efficacy in hepatic WD is fraught with frequent adverse effects resulting discontinuation. Trientine, an alternative drug has comparable efficacy in hepatic WD but has lower frequency of adverse effects. The role of ammonium tetra-thiomolybdate is presently experimental in hepatic WD. Indian childhood cirrhosis is related to excessive copper ingestion, rarely seen in present era. D-Penicillamine is effective in the early part of this disease with reversal of clinical status. Iron chelators are commonly used in secondary hemochromatosis of liver in hemolytic anemias. There are strict chelation protocols during bone marrow transplant. The role of iron chelation in neonatal hemochromatosis is presently not in vogue due to its poor efficacy and availability of other modalities of therapy. Hereditary hemochromatosis is rare in children and the use of iron chelators in this condition is limited.

Pediatric non-cirrhotic portal hypertension: Endoscopic outcome and perspectives from developing nations

Non-cirrhotic portal hypertension (NCPH) forms an important subset of portal hypertension in children. Variceal bleed and splenomegaly are their predominant presentation. Laboratory features show cytopenias (hypersplenism) and preserved hepatic synthetic functions. Repeated sessions of endoscopic variceal ligation or endoscopic sclerotherapy eradicate esophageal varices in almost all cases. After variceal eradication, there is an increased risk of other complications like secondary gastric varices, cholangiopathy, colopathy, growth failure, especially in extra-hepatic portal vein obstruction (EHPVO). Massive splenomegaly-related pain and early satiety cause poor quality of life (QoL). Meso-Rex bypass is the definitive therapy when the procedure is anatomically feasible in EHPVO. Other portosystemic shunt surgeries with splenectomy are indicated when patients present late and spleen-related issues predominate. Shunt surgeries prevent rebleed, improve growth and QoL. Non-cirrhotic portal fibrosis (NCPF) is a less common cause of portal hypertension in children in developing nations. Presentation in the second decade, massive splenomegaly and patent portal vein are discriminating features of NCPF. Shunt surgery is required in severe cases when endotherapy is insufficient for the varices. Congenital hepatic fibrosis (CHF) presents with firm palpable liver and splenomegaly. Ductal plate malformation forms the histological hallmark of CHF. CHF is commonly associated with Caroli’s disease, renal cysts, and syndromes associated with neurological defects. Isolated CHF has a favourable prognosis requiring endotherapy. Liver transplantation is required when there is decompensation or recurrent cholangitis, especially in Caroli’s syndrome. Combined liver-kidney transplantation is indicated when both liver and renal issues are present.

Peritoneal Lymphomatosis Masquerading as Pyoperitoneum in a Teenage Boy

A 16-year-old boy presented with 1 month of fever, abdominal pain, and distension. The ascitic tap drained pus-like fluid, and ultrasonography showed diffuse thickening of the omentum and mesentery with echogenic ascites. A diagnosis of pyoperitoneum due to peritoneal tuberculosis with secondary infection was suspected, and antitubercular therapy was started elsewhere, but there was no improvement. Computed tomography of the abdomen revealed enhancing soft-tissue thickening in the retroperitoneum, extending into the mesentery and encasing the superior and inferior mesenteric vessels. The ascitic fluid appearance deceptively resembled pus, but further analysis revealed atypical lymphocytes. Omental and bone marrow biopsies confirmed Burkitt lymphoma. Awareness of this rare presentation is imperative for making a correct diagnosis.

Structural basis for the modulation of the neuronal voltage-gated sodium channel NaV1.6 by calmodulin

The neuronal-voltage gated sodium channel (VGSC), Na(V)1.6, plays an important role in propagating action potentials along myelinated axons. Calmodulin (CaM) is known to modulate the inactivation kinetics of Na(V)1.6 by interacting with its IQ motif. Here we report the crystal structure of apo-CaM:Na(V)1.6IQ motif, along with functional studies. The IQ motif of Na(V)1.6 adopts an α-helical conformation in its interaction with the C-lobe of CaM. CaM uses different residues to interact with Na(V)1.6IQ motif depending on the presence or absence of Ca²⁺. Three residues from Na(V)1.6, Arg1902, Tyr1904 and Arg1905 were identified as the key common interacting residues in both the presence and absence of Ca²⁺. Substitution of Arg1902 and Tyr1904 with alanine showed a reduced rate of Na(V)1.6 inactivation in electrophysiological experiments in vivo. Compared with other CaM:Na(V) complexes, our results reveal a different mode of interaction for CaM:Na(V)1.6 and provides structural insight into the isoform-specific modulation of VGSCs.

Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit

NpmA, a methyltransferase that confers resistance to aminoglycosides was identified in an Escherichia coli clinical isolate. It belongs to the kanamycin–apramycin methyltransferase (Kam) family and specifically methylates the 16S rRNA at the N1 position of A1408. We determined the structures of apo-NpmA and its complexes with S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.4, 2.7 and 1.68 Å, respectively. We generated a number of NpmA variants with alanine substitutions and studied their ability to bind the cofactor, to methylate A1408 in the 30S subunit, and to confer resistance to kanamycin in vivo. Residues D30, W107 and W197 were found to be essential. We have also analyzed the interactions between NpmA and the 30S subunit by footprinting experiments and computational docking. Helices 24, 42 and 44 were found to be the main NpmA-binding site. Both experimental and theoretical analyses suggest that NpmA flips out the target nucleotide A1408 to carry out the methylation. NpmA is plasmid-encoded and can be transferred between pathogenic bacteria; therefore it poses a threat to the successful use of aminoglycosides in clinical practice. The results presented here will assist in the development of specific NpmA inhibitors that could restore the potential of aminoglycoside antibiotics.

Crystal structure of a fructokinase homolog from Halothermothrix orenii

Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of d-fructose to d-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrixorenii (Hore_18220 in sequence databases). The structure of the Hore_18220 protein reveals a catalytic domain with a Rossmann-like fold and a beta-sheet "lid" for dimerization. Based on comparison of Hore_18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore_18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

Dimerization of hepatitis E virus capsid protein E2s domain is essential for virus-host interaction

Hepatitis E virus (HEV), a non-enveloped, positive-stranded RNA virus, is transmitted in a faecal-oral manner, and causes acute liver diseases in humans. The HEV capsid is made up of capsomeres consisting of homodimers of a single structural capsid protein forming the virus shell. These dimers are believed to protrude from the viral surface and to interact with host cells to initiate infection. To date, no structural information is available for any of the HEV proteins. Here, we report for the first time the crystal structure of the HEV capsid protein domain E2s, a protruding domain, together with functional studies to illustrate that this domain forms a tight homodimer and that this dimerization is essential for HEV–host interactions. In addition, we also show that the neutralizing antibody recognition site of HEV is located on the E2s domain. Our study will aid in the development of vaccines and, subsequently, specific inhibitors for HEV.

Infectious viral hepatitis is a major disease in both developing and developed countries. Hepatitis E virus (HEV) is one of the major causes of severe inflammation of the liver, which is characterized by jaundice, fever, liver enlargement, and abdominal pain in humans and non-human primates. The hepatitis E virus capsid is made up of individual subunits consisting of homodimers of a single structural protein forming the virus shell. These dimers are believed to protrude from the viral surface and to interact with host cells to initiate infection. To date, no structural information is available for any of the HEV proteins. This article reports the crystal structure of the HEV capsid protein domain E2s (protruding domain), along with functional studies, which illustrate the tight homodimeric state of E2s and that dimerization is essential for both HEV–host interactions and disease progression. We also show that the neutralizing antibody recognition site of HEV is located on the E2s domain. The present findings will aid the development of vaccines and novel inhibitors for HEV.

Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein

In order to survive under extremely cold environments, many organisms produce antifreeze proteins (AFPs). AFPs inhibit the growth of ice crystals and protect organisms from freezing damage. Fish AFPs can be classified into five distinct types based on their structures. Here we report the structure of herring AFP (hAFP), a Ca(2+)-dependent fish type II AFP. It exhibits a fold similar to the C-type (Ca(2+)-dependent) lectins with unique ice-binding features. The 1.7 A crystal structure of hAFP with bound Ca(2+) and site-directed mutagenesis reveal an ice-binding site consisting of Thr96, Thr98 and Ca(2+)-coordinating residues Asp94 and Glu99, which initiate hAFP adsorption onto the [10-10] prism plane of the ice lattice. The hAFP-ice interaction is further strengthened by the bound Ca(2+) through the coordination with a water molecule of the ice lattice. This Ca(2+)-coordinated ice-binding mechanism is distinct from previously proposed mechanisms for other AFPs. However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins.

X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution

Galectins are a family of lectins which share similar carbohydrate recognition domains (CRDs) and affinity for small beta-galactosides, but which show significant differences in binding specificity for more complex glycoconjugates. We report here the x-ray crystal structure of the human galectin-3 CRD, in complex with lactose and N-acetyllactosamine, at 2.1-A resolution. This structure represents the first example of a CRD determined from a galectin which does not show the canonical 2-fold symmetric dimer organization. Comparison with the published structures of galectins-1 and -2 provides an explanation for the differences in carbohydrate-binding specificity shown by galectin-3, and for the fact that it fails to form dimers by analogous CRD-CRD interactions.

X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution

Galectins are a family of lectins which share similar carbohydrate recognition domains (CRDs) and affinity for small beta-galactosides, but which show significant differences in binding specificity for more complex glycoconjugates. We report here the x-ray crystal structure of the human galectin-3 CRD, in complex with lactose and N-acetyllactosamine, at 2.1-A resolution. This structure represents the first example of a CRD determined from a galectin which does not show the canonical 2-fold symmetric dimer organization. Comparison with the published structures of galectins-1 and -2 provides an explanation for the differences in carbohydrate-binding specificity shown by galectin-3, and for the fact that it fails to form dimers by analogous CRD-CRD interactions.

Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm

Antifreeze proteins (AFPs) adsorb to surfaces of growing ice crystals, thereby arresting their growth. The prevailing hypothesis explains the nature of adsorption in terms of a match between the hydrophilic side chains on the AFP's ice-binding surface (IBS) and the water molecules on the ice surface. The number and spatial arrangement of hydrogen bonds thus formed have been proposed to account, respectively, for the binding affinity and specificity. The crystal structure of a type III AFP from ocean pout (isoform HPLC-3) has been determined to 2.0-A resolution. The structure reveals an internal dyad motif formed by two 19-residue, loop-shaped elements. Based on of the flatness observed on the type I alpha-helical AFP's IBS, an automated algorithm was developed to analyze the surface planarity of the globular type III AFP and was used to identify the IBS on this protein. The surface with the highest flatness score is formed by one loop of the dyad motif and is identical to the IBS deduced from earlier mutagenesis studies. Interestingly, 67% of this surface contains nonpolar solvent-accessible surface area. The success of our approach to identifying the IBS on an AFP, without considering the presence of polar side chains, indicates that flatness is the first approximation of an IBS. We further propose that the specificity of interactions between an IBS and a particular ice-crystallographic plane arises from surface complementarity.

Gem-dialkyl succinic acids: a novel class of inhibitors for carboxypeptidases

gem-Dimethylsuccinic acid and its higher homolog, 2-methyl-2-ethylsuccinic acid (MESA) are highly potent inhibitors of both carboxypeptidase A (CPA) and B. The inhibition constant of MESA for CPA (0.11 microM for the racemic mixture) is remarkable considering the relatively simple structure of the compound. The molecular feature which is crucial for high affinity binding to both carboxypeptidases appears to be the nonpolar gem-dialkyl locus. The structure of the complex between MESA and CPA has been determined by X-ray crystallography to 2.0 A resolution and shows the R enantiomer of the inhibitor to be bound in a generally substrate-like manner. The carboxymethyl group is coordinated to the Zn ion in the active site, and the gem-dialkyl locus corresponds in position to the alpha-carbon of the C-terminal amino acid in a peptide substrate. The methyl group of the inhibitor occupies a cavity in the enzyme which is apparently not filled upon substrate-binding. We postulate that this cavity (the alpha-methyl hole) is designed to allow the proximal Glu-270 residue to undergo a critical movement during catalysis. The hydrophobic nature of the above cavity may play a role in modulating the reactivity of this residue. These results suggest that similar cenophilic(empty-loving) inhibitors may be found for other enzymes.

A new simple method of representing relative orientation of bases in DNA helical structures

It is shown that the strandwise correlation of the torsion angles in Nucleic acid structures can throw light on the aspects like helical distortion, in double helical and other associated forms. The single crystal X-ray coordinates for 7 A-DNA, 29 B-DNA, 8 Z-DNA and 4 tRNA structures are used to calculate the glycosyl angle chi and they are plotted in a two dimensional plot. A new torsion angle pi is defined as O4'-C1'-N1(9)-X, where X is a fictitious atom on the normal at N1(9). The chi 1 vs. chi 2 plots (where 1 and 2 refer to I and II-strand of DNA respectively) show the characteristic clustering features of A, B and Z DNAs. They are also compactly reflected in the modified graphical representation like (chi 1 + chi 2) vs. magnitude of chi 1 - chi 2 plot. chi 1 vs. chi 2 plot of the Hoogsteen type of base pairing obtained from the tRNA structures is off diagonal. The distortions due to complexing of the structures under each category, in particular, B-DNAs is readily observed. The observed points of A/B hybrid form clusters between A and B uncomplexed forms. The new torsion angle pi shows similar behavior as that of chi.

Pattern recognition approach to nucleic acid sequences

A pattern recognition method through the two dimensional matrix representation of the nucleic acids sequence is developed. This approach of two dimensional plotting primarily enables to visualize all types of bonding between different bases in a RNA or DNA. The two dimensional matrix uses the capability of intramolecular Watson-Crick type (A-U and C-G) and Wobble type (G-U) base pairing. The method discusses both parallel and anti-parallel stranded base pairing. The application of the method to tRNA is shown.

Analysis of codon usage: positional preference in various organisms

The degree of preference of the four nucleotides C, G, A and U in the three positions I, II and III of the codons of 15137 genes of various individual organisms is examined using the nucleotide sequence data obtained from the GenBank Genetic Sequence Data Bank (Release 65.0, Sep., 1990). It is found that G, A and C, are preferred maximally in the three positions respectively. Similarly, U, G and A are preferred minimally in these positions. The analysis shows a correlation in the positional base preference which discriminates against codons with the same base in all three positions or in the adjacent positions.

A unique or essentially unique single parametric characterisation of biopolymeric structures

A generalised method of characterising the three dimensional structure of any biopolymer is proposed. The method makes use of rotation and superposition of identical rigid monomeric units that comprise the polymer. Out of the various parameters involved (refers the seven parametric representation of relating two identical rigid bodies in space), the angle of rotation and superposition termed as 'phi s' turns out to be essentially unique. An ideal biopolymer with n identical rigid units is characterised by (n-1) such unique angles. In applying the results to real biopolymers, the importance of recognising that monomeric units are no more rigid but only quasi-rigid is emphasised. However, by appropriate choice of 'rigid' fraction of the quasi-rigid monomers, one is led, as first approximation, to essentially unique characterisation of the biopolymer with (n-1) such unique angles. The phi s as a function of residue number acts essentially as a finger print of the given polymeric fold and the conformation of the chosen biopolymer. However, the full set of seven parameters are needed for model building. It is emphasised that the method is general in its application to any polymer and the application of the results to proteins and nucleic acids is illustrated.