Intrinsic and Extrinsic Defect-Related Excitons in TMDCs

We investigate the excitonic peak associated with defects and disorder in low-temperature photoluminescence of monolayer transition metal dichalcogenides (TMDCs). To uncover the intrinsic origin of defect-related (D) excitons, we study their dependence on gate voltage, excitation power, and temperature in a prototypical TMDC monolayer MoS2. Our results suggest that D excitons are neutral excitons bound to ionized donor levels, likely related to sulfur vacancies, with a density of 7 × 1011 cm–2. To study the extrinsic contribution to D excitons, we controllably deposit oxygen molecules in situ onto the surface of MoS2 kept at cryogenic temperature. We find that, in addition to trivial p-doping of 3 × 1012 cm–2, oxygen affects the D excitons, likely by functionalizing the defect sites. Combined, our results uncover the origin of D excitons, suggest an approach to track the functionalization of TMDCs, to benchmark device quality, and pave the way toward exciton engineering in hybrid organic–inorganic TMDC devices

Atomic-resolution visualization and doping effects of complex structures in intercalated bilayer graphene

Molecules intercalating two-dimensional materials form complex structures that have been characterized primarily by spatially averaged techniques. Here we use aberration-corrected scanning transmission electron microscopy and density-functional-theory (DFT) calculations to study the atomic structure of bilayer graphene (BLG) and few-layer graphene (FLG) intercalated with FeCl3. In BLG, we discover two distinct intercalated structures that we identify as monolayer FeCl3 and monolayer FeCl2. The two structures are separated by atomically sharp boundaries and induce large free-carrier densities on the order of 1013cm−2 in the graphene layers. In FLG, we observe multiple FeCl3 layers stacked in a variety of possible configurations with respect to one another. Finally, we find that the microscope's electron beam can convert the FeCl3 monolayer into FeOCl monolayers in a rectangular lattice. These results reveal the need for a combination of atomically resolved microscopy, spectroscopy, and DFT calculations to identify intercalated structures and study their properties

<i>Mycobacterium tuberculosis</i> Cyclophilin A Uses Novel Signal Sequence for Secretion and Mimics Eukaryotic Cyclophilins for Interaction with Host Protein Repertoire

<div><p>Cyclophilins are prolyl isomerases with multitude of functions in different cellular processes and pathological conditions. Cyclophilin A (PpiA) of <i>Mycobacterium tuberculosis</i> is secreted during infection in intraphagosomal niche. However, our understanding about the evolutionary origin, secretory mechanism or the interactome of <i>M. tuberculosis</i> PpiA is limited. This study demonstrates through phylogenetic and structural analyses that PpiA has more proximity to human cyclophilins than the prokaryotic counterparts. We report a unique N-terminal sequence (MADCDSVTNSP) present in pathogenic mycobacterial PpiA and absent in non-pathogenic strains. This sequence stretch was shown to be essential for PpiA secretion. The overexpression of full-length PpiA from <i>M. tuberculosis</i> in non-pathogenic <i>Mycobacterium smegmatis</i> resulted in PpiA secretion while truncation of the N-terminal stretch obstructed the secretion. In addition, presence of an ESX pathway substrate motif in <i>M. tuberculosis</i> PpiA suggested possible involvement of Type VII secretion system. Site-directed mutagenesis of key residues in this motif in full-length PpiA also hindered the secretion in <i>M. smegmatis</i>. Bacterial two-hybrid screens with human lung cDNA library as target were utilized to identify interaction partners of PpiA from host repertoire, and a number of substrates with functional representation in iron storage, signal transduction and immune responses were detected. The extensive host interactome coupled with the sequence and structural similarity to human cyclophilins is strongly suggestive of PpiA being deployed by <i>M. tuberculosis</i> as an effector mimic against the host cyclophilins.</p></div

Identification of a novel signal sequence in pathogenic mycobacterial PpiA.

<p><b>Fig. 4A</b>: A phylogram of mycobacterial PpiA type cyclophilins revealed the coalescing of pathogenic mycobacteria (red) into a clade, different than that of non-pathogenic mycobacteria (black). <b>Fig. 4B</b>: Sequence alignment of the N-terminal stretch revealed that the proposed signal sequence present in pathogenic mycobacterial PpiA was either missing or mismatched in non-pathogenic species. <b>Fig. 4C</b>: Sequence logo analysis of the N-terminal stretch of the mycobacterial PpiA type cyclophilins.</p

Mycobacterial proteins interacting with PpiA in pull-down assays.

<p>Mycobacterial proteins interacting with PpiA in pull-down assays.</p

Substrates of PpiA identified from mammalian cell lysates.

<p>Substrates of PpiA identified from mammalian cell lysates.</p

Identification of interaction partners of PpiA in human lung cDNA repertoire by BacterioMatch® two-hybrid screens.

<p>Identification of interaction partners of PpiA in human lung cDNA repertoire by BacterioMatch® two-hybrid screens.</p

Demonstration of <i>M. tuberculosis</i> PpiA secretion and localization.

<p>Immunoblotting was performed to show differential secretion pattern of overexpressed full-length, truncated and YD-ESX mutant forms of <i>M. tuberculosis</i> PpiA in the culture filtrates of <i>M. smegmatis</i>. <b>Fig. 5A</b>: Presence of overexpressed full-length, truncated and YD ESX mutant PpiA in the whole cell lysates (CL) of <i>M. smegmatis</i> (left upper panel). Secretion of overexpressed full-length PpiA is evident in <i>M. smegmatis</i> culture filtrate (CF) while the truncated PpiA without the proposed signal sequence and YD ESX mutant PpiA, though expressed, is not secreted (left lower panel). Expression of Ag85 homolog in all culture filtrates as a control for secretion (right upper panel) and expression of GroEl1 as a cell lysis control and (right lower panel). 12% SDS-PAGE was used in all these blots. <b>Fig. 5B</b>: Truncated PpiA and YD-ESX mutant PpiA showed very little amount of secretion even in two-fold culture filtrate concentrate with respect to the full-length PpiA culture filtrate. 16% SDS-PAGE was overrun to distinguish the size difference in these blots. Cell lysate (CL) fractions with two-fold concentrated amount of truncated and YD ESX mutant PpiA, top panel; Equal concentration of all culture filtrates, middle panel; and Culture filtrate fractions with two fold concentrate of truncated and YD ESX mutant PpiA, bottom panel. <b>Fig. 5C</b>: Immunoelectron micrograph showing localization of secreted full-length PpiA overexpressed in <i>M. smegmatis</i> in comparison with pVV16 vector control in <i>M. smegmatis</i>. Arrows indicate the position of PpiA. T.S: Transverse section, L.S: Longitudinal section.</p

Structural and immunoinformatics analysis of <i>M. tuberculosis</i> PpiA.

<p><b>Fig. 3A</b>: Structural overlapping of <i>M. tuberculosis</i> PpiA (green) with human PPWD1 (yellow) demonstrated almost complete overlap, (inset showing the loop region). <b>Fig. 3B</b>: Comparative analysis of structural overlapping between <i>M. tuberculosis</i> PpiA (green) with human PPWD1 (yellow) as well as with <i>E. coli</i> PpiA (red), respectively, revealed a poor overlap with the prokaryotic cyclophilin. <b>Fig. 3C</b>: Structural overlapping of <i>M. tuberculosis</i> PpiA (green) and four human cyclophilins (HPPWD1, HPPIAL3, HPPIC, HPPIA) by Chimera program showed almost complete overlap apart from a region of difference (in form of a loop) in <i>M. tuberculosis</i> PpiA. <b>Fig. 3D</b>: Multiple sequence alignment of the human cyclophilins and <i>M. tuberculosis</i> PpiA identified the region of difference ‘AQGTKDYSTQNASGGP’ (inset, black-bordered box). <b>Fig. 3E</b>: Immunoinformatics analysis using ABCpred software identified putative epitopic regions in <i>M. tuberculosis</i> PpiA.</p

Phylogenetic analysis of cyclophilins.

<p>A circular phylogram representation of the cyclophilin sequences collected from various taxa. <i>M. tuberculosis</i> PpiA is grouped with eukaryotic and actinobacterial counterparts quite distinct from the prokaryotic clades of cyclophilins. The colored labels are used as follows: human cyclophilins – green, <i>M. tuberculosis</i> and <i>Mycobacterium leprae</i> PpiA – red, <i>M. tuberculosis</i> and <i>M. leprae</i> PpiB – brown, <i>E. coli</i> cyclophilins – pink and selected gut microbial cyclophilin – dark blue.</p