Rapid detection of rifampicin resistance in Mycobacterium tuberculosis by high-resolution melting curve analysis

SETTING

High-resolution melting curve analysis (HRMA) can be used to screen for mutations in genes without the need for specific probes, with low turnaround time and high cost-effectiveness.

OBJECTIVE

To detect the sensitivity and specificity of a line-probe assay (LPA) and HRMA in comparison with BACTEC™ MGIT™ 960 for the detection of rifampicin (RMP) resistance.

DESIGN

A total of 219 Mycobacterium tuberculosis isolates tested by MGIT 960 for RMP susceptibility were tested with HRMA and LPA. Discordant samples were processed for sequencing of the RMP resistance-determining region (RRDR) of the rpoB gene.

RESULTS

HRMA identified 93 of 103 (90.3%) isolates that were resistant and 113/116 (97.4%) that were susceptible on MGIT 960, with a sensitivity and specificity of respectively 90.3% and 97.4%. HRMA identified 117/119 (98.3%) LPA-susceptible and 94/100 (94%) resistant isolates, with 98.3% specificity and 94% sensitivity. Two isolates that were susceptible on LPA but resistant on HRMA showed silent mutations at 539 and 541 codons on sequencing, while 6 isolates that were susceptible on HRMA but resistant on LPA showed D516V (n = 4) and H526C/D (n = 2) mutations. Four isolates (3.9%) that were resistant on MGIT were susceptible on all three genotypic methods, which could be due to mutations outside the RRDR or efflux pumps.

CONCLUSION

HRMA shows good potential as a rapid screening tool for the detection of drug resistance.

Molecular Characterization of Buffalo Haptoglobin: Sequence Based Structural Comparison Indicates Convergent Evolution Between Ruminants and Human

Haptoglobin (Hp) protein has high affinity for hemoglobin (Hb) binding during intravascular hemolysis and scavenges the hemoglobin induced free radicals. Earlier reports indicate about uniqueness of Hp molecule in human and cattle, but in other animals, it is not much studied. In this paper, we characterized buffalo Hp molecule and determined its molecular structure, evolutionary importance, and tissue expression. Comparative analysis and predicted domain structure indicated that the buffalo Hp has an internal duplicated region in α-chain only similar to an alternate Hp2 allele in human. This duplicated part encoded for an extra complement control protein CCP domain. Phylogenetic analysis revealed that buffalo and other ruminants were found to group together separated from all other non-ruminants, including human. The key amino acid residues involved in Hp and Hb as well as Hp and macrophage scavenger receptor, CD163 interactions in buffalo, depicted a significant variation in comparison to other non-ruminant species. Constitutive expression of Hp was also confirmed across all the vital tissues of buffalo, for the first time. Results revealed that buffalo Hp is both structurally and functionally conserved, having internal duplication in α-chain similar to human Hp2 and other ruminant species, which might have evolved separately as a convergent evolutionary process. Furthermore, the presence of extra Hp CCP domain possibly in all ruminants may have an effect during dimerization of molecule in these species.

Inverted papilloma of the hard palate masquerading as a carcinoma

Inverted papilloma (IP) is a rare, benign tumor of the nose and paranasal sinus. However, it is locally aggressive, the recurrence rate is high and malignant transformation is possible. Until now, IP of the hard palate has rarely been reported in the literature. Here, we reported a case with IP of the hard palate, which clinically presented as a carcinomatous growth. The management of IP is complete surgical excision with a close follow-up to detect early recurrence and/or malignant transformation.

Confirmation of TTC8 as a disease gene for nonsyndromic autosomal recessive retinitis pigmentosa (RP51)

Nonsyndromic retinitis pigmentosa (RP) is genetically highly heterogeneous, with >100 disease genes identified. However, mutations in these genes explain only 60% of all RP cases. Blood samples were collected from 12 members of an autosomal recessive RP family. Whole genome homozygosity mapping and haplotype analysis placed the RP locus in this family at chromosome 14q31.3. Whole-exome sequencing (WES) in proband revealed a mutation in TTC8, which was flagged as most likely candidate gene by bioinformatic analysis. TTC8 is mutated in Bardet-Biedl syndrome 8 (BBS8), and once reported previously in a family with nonsyndromic RP. Sequencing of amplified products of exon 13 of TTC8 validated c.1347G>C (p.Gln449His), a novel change that affects the final nucleotide of exon 13 and might deleteriously affect splicing. This mutation segregated completely with the disease in the family and was not observed in 100 ethnically matched controls from same population. This represents second report of a TTC8 mutation in nonsyndromic RP, thus confirming the identity of TTC8 as causative gene for RP51.

MARKER ASSISTED EVALUATION OF MORPHOLOGICAL AND GENETIC ATTRIBUTES OF SUB-POPULATIONS OF NILI-RAVI BUFFALO: A VULNERABLE DAIRY TYPE RIVERINE BREED OF INDIA

In the present study, we report the distribution of true to type and atypical Nili-Ravi buffalo, a vulnerable dairy type riverine breed of North India and its underlying genetic structure. Out of total investigated buffaloes 73.5% had bilateral wall eyes while 5.4% had unilateral wall eyes and 21.1% had no wall eyes. 41.15% of Nili-Ravi buffaloes maintained in the breeding farm were having typical true to the type characteristics (both eyes walled, white markings in forehead, muzzle/chin, all the four legs and tail) while only 28.5% of Nili-Ravi buffaloes were true to the type under field conditions. Genotypic data were generated in four groups of Nili-Ravi buffalo (FMTNR--Typical Nili-Ravi from farm; FMANR--Atypical Nili-Ravi from farm; FDTNR--Typical Nili-Ravi from field; FDANR--Atypical Nili-Ravi from field) at 16 microsatellite loci. Comparative genetic analysis of various groups of Nili-Ravi buffaloes with Murrah revealed significant between group differences with an estimated global F(ST) of 0.063. Pair-wise F(ST) values ranged from 0.003 (between FDTNR and FDANR) to 0.112 (between FMTNR and FDTNR). Phylogenetic analysis and multi-dimensional scaling revealed clustering of FDTNR and FDANR together while FMTNR and FMANR clustered separately with Murrah in between farm and field Nili-Ravi buffaloes. Based on the results, the paper also proposes three pronged strategy for conservation and sustainable genetic improvement of Nili-Ravi buffalo in India.

Comparison of the Effects of Zonisamide, Ethosuximide and Pregabalin in the Chronic Constriction Injury Induced Neuropathic Pain in Rats

Background:

Evidence has been generated that various anticonvulsant agents provide relief of several chronic pain syndromes and therefore as an alternative to opioids, nonsteroidal anti-inflammatory, and tricyclic antidepressant drugs in the treatment of neuropathic pain. The results of these studies thus raise the question of whether all anticonvulsant drugs or particular mechanistic classes may be efficacious in the treatment of neuropathic pain syndromes.

Aim:

The aim was to compare the clinically used anticonvulsant drugs which are differ in their mechanism of action in a chronic pain model, the chronic constriction injury, in order to determine if all anticonvulsants or only particular mechanistic classes of anticonvulsants are analgesic.

Materials and Methods:

The study included zonisamide, ethosuximide and pregabalin. All compounds were anticonvulsant with diverse mechanism of actions. The peripheral neuropathic pain was induced by chronic constriction injury of the sciatic nerve in male Sprague-Dawley rats. Zonisamide (80 and 40 mg/kg), ethosuximide (300 and 100 mg/kg), pregabalin (50 and 20 mg/kg), and saline was administered intraperitoneally in respective groups in a blinded, randomized manner from postoperative day (POD) 7-13. Paw withdrawal duration to spontaneous pain, chemical allodynia and mechanical hyperalgesia and paw withdrawal latency to mechanical allodynia and thermal hyperalgesia were tested before drug administration on POD7 and after administration on POD 7, 9, 11 and 13.

Results:

The present study suggests that these drugs could provide an effective alternative in the treatment of neuropathic pain. However, zonisamide and pregabalin appears to have suitable efficacy to treat a wide spectrum of neuropathic pain condition.

Conclusion:

The present findings suggest that the inhibition of N-type calcium channels or voltage-gated sodium and T-type calcium channels provides better analgesic potential instead of inhibition of T-type calcium channels alone.

Magnetic sentinel node and occult lesion localization in breast cancer (MagSNOLL Trial)

BACKGROUND

Non-palpable breast cancers require localization-guided surgery and axillary staging using sentinel lymph node biopsy (SLNB). This study investigated the novel technique of magnetic-guided lesion localization and concurrent SLNB, which avoids the need for wire-guided localization and radioisotopes.

METHODS

An ultrasound-guided intratumoral injection of magnetic tracer (0·5 ml) was performed in a protocol-driven predefined minimum of ten patients with palpable breast cancer to assess the ability of the magnetic tracer safely to localize the tumour at the site of injection and concurrently drain to the lymphatics. Once successful lesion localization had been confirmed (peak magnetometer count retained at the centre of the tumour), the technique was undertaken in a further 20 patients with non-palpable breast cancers awaiting wide local excision and SLNB. All patients underwent SLNB with both the magnetic and standard dual (radioisotope and Patent Blue V dye) techniques.

RESULTS

Thirty-two patients were recruited, of whom 12 (1 with bilateral disease) presented with palpable and 20 with non-palpable breast cancer. Peak magnetometer counts were retained at the tumour centre in all palpable (13) and non-palpable (20) breast cancers. Re-excisions for involved margins were necessary in two patients with non-palpable breast cancers. The sentinel lymph node identification rates were 28 of 33 procedures for the magnetic technique alone, 32 of 33 for the magnetic technique combined with blue dye, and 32 of 33 for the standard dual technique.

CONCLUSION

Magnetic lesion localization is feasible, with intratumoral magnetic tracer injection combined with a periareolar injection of blue dye for subsequent SNLB.

Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north-east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia.