Beyond Rattling: Tetrahedrites as Incipient Ionic Conductors.

Materials with ultralow thermal conductivity are crucial to many technological applications, including thermoelectric energy harvesting, thermal barrier coatings, and optoelectronics. Liquid-like mobile ions are effective at disrupting phonon propagation, hence suppressing thermal conduction. However, high ionic mobility leads to the degradation of liquid-like thermoelectric materials under operating conditions due to ion migration and metal deposition at the cathode, hindering their practical application. Here, a new type of behavior, incipient ionic conduction, which leads to ultralow thermal conductivity, while overcoming the issues of degradation inherent in liquid-like materials, is identified. Using neutron spectroscopy and molecular dynamics (MD) simulations, it is demonstrated that in tetrahedrite, an established thermoelectric material with a remarkably low thermal conductivity, copper ions, although mobile above 200 K, are predominantly confined to cages within the crystal structure. Hence the undesirable migration of cations to the cathode can be avoided. These findings unveil a new approach for the design of materials with ultralow thermal conductivity, by exploring systems in which incipient ionic conduction may be present.

Lone Pair Rotation and Bond Heterogeneity Leading to Ultralow Thermal Conductivity in Aikinite.

Understanding the relationship between the crystal structure, chemical bonding, and lattice dynamics is crucial for the design of materials with low thermal conductivities, which are essential in fields as diverse as thermoelectrics, thermal barrier coatings, and optoelectronics. The bismuthinite-aikinite series, Cu1-x□xPb1-xBi1+xS3 (0 ≤ x ≤ 1, where □ represents a vacancy), has recently emerged as a family of n-type semiconductors with exceptionally low lattice thermal conductivities. We present a detailed investigation of the structure, electronic properties, and the vibrational spectrum of aikinite, CuPbBiS3 (x = 0), in order to elucidate the origin of its ultralow thermal conductivity (0.48 W m-1 K-1 at 573 K), which is close to the calculated minimum for amorphous and disordered materials, despite its polycrystalline nature. Inelastic neutron scattering data reveal an anharmonic optical phonon mode at ca. 30 cm-1, attributed mainly to the motion of Pb2+ cations. Analysis of neutron diffraction data, together with ab-initio molecular dynamics simulations, shows that the Pb2+ lone pairs are rotating and that, with increasing temperature, Cu+ and Pb2+ cations, which are separated at distances of ca. 3.3 Å, exhibit significantly larger displacements from their equilibrium positions than Bi3+ cations. In addition to bond heterogeneity, a temperature-dependent interaction between Cu+ and the rotating Pb2+ lone pair is a key contributor to the scattering effects that lower the thermal conductivity in aikinite. This work demonstrates that coupling of rotating lone pairs and the vibrational motion is an effective mechanism to achieve ultralow thermal conductivity in crystalline materials.

Abundance of New Delhi Metallo-ß-Lactamase-Producing Acinetobacter, Escherichia, Proteus, and Pseudomonas spp. in Mahananda and Karala Rivers of India.

In this study, we report a high incidence of New Delhi metallo-ß-lactamase (NDM)-producing and ampicillin-catabolizing bacteria within carbapenem-resistant bacterial populations in the waters of two important rivers, Mahananda and Karala, bisecting two most populous towns, Siliguri and Jalpaiguri, respectively, in the northern West Bengal, India. Isolates producing NDM belonged to four genera, Acinetobacter, Escherichia, Proteus, and Pseudomonas; among which few were phylogenetically determined as putatively novel species. Class 1 integrons with the frequent presence of aadA and aac(6')-Ib gene cassettes in 50% of NDM-bearing isolates are indicative of possible selective pressures generated out of unregulated use of streptomycin, in agriculture practiced by the cultivators and tea planters living in locales drained by these two rivers, in their up- and downstream, and amikacin in the most crowded government-sponsored "sadar" and district hospitals of Siliguri and Jalpaiguri. NDM-delivering bacteria in rivers have genuine consequences for city inhabitants who are dependent on public water and sanitation facilities. Standard reconnaissance of antibiotic resistance, consolidating ecological sampling just as the assessment of clinical isolates, should be set up as a need.

Pandrug-resistant Pseudomonas sp. expresses New Delhi metallo-ß-lactamase-1 and consumes ampicillin as sole carbon source.

OBJECTIVES: This study aims to investigate ampicillin catabolism in a pandrug-resistant strain, Pseudomonas sp. MR 02 of P. putida lineage. METHODS: The characterization of carbapenem resistance was done following the standard protocol. The broth macrodilution method was used to determine the MIC values of antimicrobial agents both in the presence and in the absence of phenylalanine-ß-naphthylamide. High MIC values (>10 000 mg/L) of ampicillin led to speculation that it may serve as a growth substrate, and thus minimal medium was used to evaluate ampicillin as a nutrient. The growth of MR 02 was measured in minimal medium in the presence or absence of 0.4 mM EDTA, supplemented with ampicillin as sole carbon, nitrogen and energy source. RNA-seq was used to generate expression profiles of genes in ampicillin or glucose-grown cells. The blaNDM-1 gene of MR 02 was cloned in the pHSG398 vector and expressed in Escherichia coli DH5α. RESULTS: Phenotypic analysis along with genome sequence data identifies Pseudomonas sp. MR 02 as a pandrug-resistant strain. Transcriptome data has revealed that blaNDM-1 was among the top 50 differentially expressed genes in ampicillin grown cells compared to the glucose grown cells in the minimal medium. Heterologous expression of blaNDM-1 gene in E. coli DH5α enabled its growth and subsistence on ampicillin as the sole source of carbon and energy. DISCUSSION: The ability of a pandrug-resistant Pseudomonas sp. MR 02 to consume ampicillin for growth has a huge implication in the bioremediation of ß-lactam residues in the environment.

Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus.

To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in GISAID till 21 August 2020. Globally, nsp1/nsp2 and orf7a/orf3a were the most mutation-ridden non-structural and structural genes respectively. Phylogeny of 4618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries, including India, whereas the recently-derived lineages are more globally distributed. Of the total 20,163 instances of polymorphism detected across global genomes, 12,594 and 7569 involved transitions and transversions, predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not the non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host metabolism, while it is still redefining virulence/transmissibility strategies at the molecular level. Mechanistic bases and evolutionary/pathogenicity-related implications are discussed for the predominant mutation-types.

Investigation on the structure and thermoelectric properties of CuxTe binary compounds.

Cu2Te is a superionic conductor that belongs to the Phonon Liquid Electron Crystal class of thermoelectric (TE) materials. Despite the simple chemical formula, the crystal structures and phases in the Cu2Te system have not been understood properly. In this work, we study the structural and TE properties of Cu2Te (CT2), Cu1.6Te (CT1.6) and Cu1.25Te (CT1.25). The samples were synthesized via a solid-state reaction method. Powder X-ray diffraction analysis revealed that the samples have different crystal structures depending upon the Cu : Te stoichiometry. The elemental compositional analysis showed that all the samples are copper deficient. This is due to the precipitation of metallic copper on the surface of the ingot arising from the thermal dissociation of Cu2Te. The transport properties were measured in the temperature range 300 K-600 K. The electrical conductivity (σ) decreases with an increase in temperature indicating a metal-like behaviour for all the samples. The positive Seebeck coefficients (S) for all the samples indicates that majority charge carriers are holes. The sample CT2 has a higher S (29.5 µV K-1 at 573 K) and a lower σ (2513 S cm-1 at 573 K) due to a lower carrier (hole) concentration compared to the other two samples. With the increase in Cu deficiency, the hole concentration increases, and this leads to higher electronic thermal conductivity in the samples CT1.6 and CT1.25. The maximum thermoelectric figure of merit of 0.03 at 524 K is achieved for the sample CT2 owing to its higher power factor (0.24 mW m-1 K-2) and lower thermal conductivity (3.8 W m-1 K-1). The present study bridges the gap between the theoretical predictions and experimental observations involving the various possible structures in this system. Furthermore, we have shown that the Cu vacancies are detrimental to the thermoelectric performance of Cu2Te.

Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India.

The draft genome sequence of a novel strain, Pseudomonas sp. MR 02, a pyomelanin-producing bacterium isolated from the Mahananda River at Siliguri, West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb, with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean gene length, 923 bp), among which 5,503 are protein-coding genes, including the genes required for the catabolism of tyrosine or phenylalanine for the characteristic production of homogentisic acid (HGA). Excess HGA, on excretion, auto-oxidizes and polymerizes to form pyomelanin.

Diverse gene cassettes in class 1 integrons of facultative oligotrophic bacteria of River Mahananda,West Bengal, India.

BACKGROUND: In this study a large random collection (n=2188) of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007-2009) from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products. METHODOLOGY/PRINCIPAL FINDINGS: Replica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19%) were antibiotic-resistant comprising of both single-antibiotic resistance (SAR) and multiple-antibiotic resistant (MAR), and 521 (23.81%) were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s) of varying sizes from 0.15 to 3.45 KB. Chi-square (χ(2)) test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6'-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families, Moraxellaceae, Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. CONCLUSIONS: Oligotrophic bacteria are good sources of novel genes as well as potential reservoirs of antibiotic resistance gene casettes.

Characterization of a novel trimethoprim resistance gene, dfrA28, in class 1 integron of an oligotrophic Acinetobacter johnsonii strain, MB52, isolated from River Mahananda, India.

The present work has validated the capability of using diluted Luria broth (10(-3)) and its amendment with antibiotics to quantify proportions of antibiotic-resistant oligotrophic bacteria contained in river water. The assay conditions for assessing fractions of antibiotic-resistant oligotrophic bacteria, especially the type and concentration of antibiotic exposure by determining LD(50) concentration for each antibiotic using sensitive oligotrophic strain, have been standardized. The presence of an array of two gene cassettes including a novel dihydrofolate reductase gene, dfrA28, within the variable region of the class 1 integron in an oligotrophic test strain, MB52, in a population of oligotrophic bacteria isolated from Mahananda River water, has been described. The predicted protein consisting of 172 amino acids exhibited 76.4% amino acid identity with DfrA1. A gene for streptomycin resistance, aminoglycoside adenyl transferase aadA1, was located downstream of dfrA28. Phylogenetic analysis of MB52 identified it as a strain of Acinetobacter johnsonii.

Conjugation potential and class 1 integron carriage of resident plasmids in river water copiotrophs.

Plasmid content was investigated in hundred copiotrophic Gram-negative river water isolates that exhibited resistance to four or more antibiotics. A total of seventy-seven isolates were found to carry plasmids of varying sizes. These isolates were primarily grouped as Pseudomonads and members of Enterobacteriaceae on the basis of physiological and biochemical tests. Fifty-six isolates that were rifampicin-sensitive and belonged to Enterobacteriaceae family were chosen as donors for the conjugal transfer assay. Eighteen of the isolates successfully transferred conjugable plasmids to the E. coli DH5alpha recipient. Countable multiple antibiotic resistant transconjugants arose readily and conjugal transfer frequency was in the range of 3.75 x 10(-6) to 1.0 x 10(-1). The most common carriage of resistances conferred by transmissible R plasmids was against ampicillin, cefotaxim and cephalexin. The residence of class 1 integrons on conjugative R plasmids was confirmed in only six transconjugants. Gene cassettes borne on the integrons were identified to be dihydrofolate reductases (dhfrs). The major concern of this study was about the copiotrophs containing self-transmissible R plasmids which may be potential reservoirs of antibiotic-resistance genes and instrumental in dissemination of the same in the environment.

Incidence of class 1 integrons in multiple antibiotic-resistant Gram-negative copiotrophic bacteria from the River Torsa in India.

The presence of class 1 integrons in multiple-antibiotic-resistant (MAR) Gram-negative copiotrophic bacteria from the River Torsa in India was detected using a polymerase chain reaction (PCR)-based screening method. Among 100 isolates that were resistant to at least five of the twelve antibiotics tested, 40 carried class 1 integrons, with inserted DNA regions of 0.7-3.2 kb. Carriage of integrons in strains of higher MAR index was found to be statistically significant. DNA sequencing was used to identify the genetic content of the integron-variable regions. In addition to the identification of gene cassettes dfrA1, dfrA5, dfrA7, dfrA17 and a variant of dfrA12 for trimethoprim, aac(6')-Ib for amikacin and tobramycin and aadA1 and aadA6 for streptomycin and spectinomycin resistance, a novel ORF predicted from a sequence of Morganella sp. TR 90 bearing homology with the Vibrio cholerae dfrA1 gene cassette was characterized. To our knowledge, this is the first report of the incidence and abundance of class 1 integrons in copiotrophic river water bacteria from India.

Unregulated use of antibiotics in Siliguri city vis-a-vis occurrence of MAR bacteria in community waste water and river Mahananda, and their potential for resistance gene transfer.

The unregulated use of antibiotics, including therapeutic and prophylactic prescribing, in the fastest growing city of West Bengal, Siliguri, was studied indirectly from a random survey conducted on retail medicine sellers at their counters. Ciprofloxacin, ampicillin, norfioxacin and amoxycillin were the highest retailed antibiotics and 58% of the city pharmacies sold antibiotics even without prescriptions. To understand the influence of the extent of antibiotic use by the community on the collective bacterial flora in the aquatic environment, we have determined the fraction(s) of Standard Plate Count (SPC) bacteria resistant to different antibiotics and multiple antibiotic resistance (MAR) profile of resistant SPC isolates from two municipal open drains and Mahananda river water samples of Siliguri. Within the MAR groups of Drain I and Drain II samples, 37.44% and 77.43% respectively were resistant to all seven antibiotics (ampicillin, chloramphenicol, ciprofloxacin, kanamycin, netilmicin, streptomycin and tetracycline) used in the study. Twenty Gram-negative SPC MAR isolates were examined for the presence of plasmids. Antibiotic resistance was shown to be associated with a carriage of a 47 kb (D1QN - 9), 48 kb (D2QN - 14) and 49.4 and 3.6 kb (MR - 1) plasmids, which were transmissible to the Escherichia coli DH5alpha recipient. The rapid spread of antibiotic resistance genes in bacterial population as a consequence of indiscriminate use of antibiotics, which can be partly attributed to plasmid-mediated horizontal transfer was discussed.

Physico-chemical and bacteriological investigation on the River Torsa of North Bengal.

A few physico-chemical and bacteriological parameters on certain locations of the river Torsa was studied. The major characteristics of Torsa river water were high alkalinity, high concentration of free ammonia with respect to albuminoid ammonia and the presence of bacteria of fecal origin. Marked seasonal variations of the parameters were also observed.