The Human Bone Collection of the Faculty of Dentistry at the University of Hong Kong: History and description of cranial and postcranial skeletal remains.

OBJECTIVES: The present work describes the status and contents of The Human Bone Collection of the Faculty of Dentistry at the University of Hong Kong. MATERIALS AND METHODS: The Collection originates from the 1980s and became officially established in 2017 for teaching and research purposes. Most of the Collection consists of unclaimed human remains of southern Chinese individuals exhumed from local cemeteries and donated to the Faculty in the last few decades. The demographic information was provided largely from burial records and forensic estimations. Since 2016, the Collection has undergone a process of reorganization into cranial and postcranial remains, followed by preservation procedures that included cleaning and classification. RESULTS: The Collection currently consists of remains belonging to about 368 individuals (243 males, 54 females, 71 unknown), with ages ranging from 0.8 to 90 years (mean 57.4 years). It comprises cranial remains belonging to 260 individuals (169 males, 39 females, 52 unknown), and postcranial remains belonging to 248 individuals (180 males, 42 females, 26 unknown). The preservation status ranges from poor to good, with the cranial remains better preserved than the postcranial elements. For a large number of individuals, ear ossicles, soil samples, and other materials are also available. DISCUSSION: The Collection is accessible to local and international institutions for teaching and research.

Rare/cryptic Aspergillus species infections and importance of antifungal susceptibility testing.

BACKGROUND: The number of patients infected with Aspergillus rose dramatically in recent years. However, studies on the clinical spectrum and antifungal susceptibilities of non-classical (non-fumigatus, non-flavus, non-niger and non-terreus) pathogenic Aspergillus species are very limited. OBJECTIVES: We examined the clinical spectrum and antifungal susceptibilities of 34 non-duplicated, non-classical Aspergillus isolates collected from Hong Kong, Shenzhen and Shanghai. METHODS: The Aspergillus isolates were identified by internal transcribed spacer, partial BenA and partial CaM sequencing and phylogenetic analyses. Susceptibility testing against eight antifungals was performed following the European Committee for Antimicrobial Susceptibility Testing's methodology. RESULTS: The 34 Aspergillus isolates were identified as 14 different rare/cryptic species of four sections (Flavi [n = 8], Nidulantes [n = 8], Nigri [n = 17] and Restricti [n = 1]). Except for one patient whose clinical history could not be retrieved, 72.7% of the remaining patients had underlying conditions predisposing them to Aspergillus infections. The most common diseases were pulmonary infections (n = 15), followed by skin/nail infections (n = 6), chronic otitis externa and/or media (n = 5), wound infections (n = 2) and mastoiditis/radionecrosis (n = 1), while three were colonisations. Five patients succumbed due to the infections during the admission, and another two died 5 years later because of chronic pulmonary aspergillosis. Antifungal susceptibility testing showed that they possessed different susceptibility profiles compared to the classical Aspergillus species. The majority of isolates characterised were sensitive or wild-type to amphotericin B. The minimum effective concentrations for all the three echinocandins were also low. CONCLUSION: Susceptibility testing should be performed for infections due to these rare/cryptic Aspergillus species to guide proper patient management.

Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

Atomic force microscopy with nanoscale cantilevers resolves different structural conformations of the DNA double helix.

Structural variability and flexibility are crucial factors for biomolecular function. Here we have reduced the invasiness and enhanced the spatial resolution of atomic force microscopy (AFM) to visualize, for the first time, different structural conformations of the two polynucleotide strands in the DNA double helix, for single molecules under near-physiological conditions. This is achieved by identifying and tracking the anomalous resonance behavior of nanoscale AFM cantilevers in the immediate vicinity of the sample.

Imaging surface charges of individual biomolecules.

Surface charges play a key role in determining the structure and function of proteins, DNA, and larger biomolecular structures. Here we report on the measurement of the electrostatic surface potential of individual DNA and avidin molecules with nanometer resolution using Kelvin probe force microscopy. We also show, for the first time, the surface potential of buffer salts shielding individual DNA molecules, which would not be possible with conventional ensemble techniques.

Immobilisation of proteins by atomic clusters on surfaces.

In this Opinion article, we describe a nanotechnology-based approach to immobilize and orient proteins onto surfaces using atomic clusters prepared by physical methods. This is relevant to future protein biochips where dilute arrays of protein binding sites, each designed to immobilize no more than one protein molecule, would be ideal. In the case of a surface consisting of size-selected atomic gold clusters, proteins containing free cysteine residues can chemisorb directly to the bare cluster surface, thus effecting oriented immobilisation. The selection of atomic gold clusters in the size range 1-100 atoms (<3nm in diameter) is intended to ensure that, typically, only one protein can bind directly to the cluster surface. These nanoclusters of a smaller size scale than that of the protein present minimal contact between the gold and the protein, and hence imply a reduced risk of protein denaturing compared with gold films or extended surfaces.

Accuracy of radiographic measurements for implant planning using cone-beam and helical computer tomography.

AIM: The aim of the present study was to compare the accuracy of radiographic measurements for dental implants planning using cone-beam computed tomography (CBCT) and helical computed tomography (HCT). METHODS: Six pig ribs were wrapped by putty impression material, with radiographic markers placed. Two CBCT and an HCT were taken following the standard protocols. Twenty-five locations were selected, with vertical and horizontal dimensions measured using the default software, as well as on the processed HCT films by a digital caliper. The actual dimensions of the ribs measured by the digital caliper served as the control. Differences between radiographic dimensions and the actual dimensions were tested by two-way analysis of variance. RESULTS: No differences were found between measurements made by CBCT and HCT images using the default software (P > 0.05). However, both measurements were statistically-significantly lower than the control (P < 0.001), and the mean difference was 0.3 mm. Measurements made on HCT films were statistically-significantly greater than the control (P < 0.001), and the mean difference was 0.5 mm. CONCLUSION: The accuracy of CBCT and HCT are similar, and both are reliable tools for implant planning. It is preferable to perform the planning using default software, rather than making direct measurements on films.

Real-time visualization of perforin nanopore assembly.

Perforin is a key protein of the vertebrate immune system. Secreted by cytotoxic lymphocytes as soluble monomers, perforin can self-assemble into oligomeric pores of 10-20 nm inner diameter in the membranes of virus-infected and cancerous cells. These large pores facilitate the entry of pro-apoptotic granzymes, thereby rapidly killing the target cell. To elucidate the pathways of perforin pore assembly, we carried out real-time atomic force microscopy and electron microscopy studies. Our experiments reveal that the pore assembly proceeds via a membrane-bound prepore intermediate state, typically consisting of up to approximately eight loosely but irreversibly assembled monomeric subunits. These short oligomers convert to more closely packed membrane nanopore assemblies, which can subsequently recruit additional prepore oligomers to grow the pore size.

Residue-specific immobilization of protein molecules by size-selected clusters.

The atomic force microscope (AFM), operating in contact mode, has been employed in buffer solution to study two proteins; (i) green fluorescent protein (GFP), from the hydromedusan jellyfish Aequorea victoria; and (ii) human oncostatin M (OSM), in the presence of size-selected gold nanoclusters pinned on to a highly oriented pyrolytic graphite substrate. The AFM images have revealed immobilization of single molecules of OSM, which are strongly bound to the gold nanoclusters. Conversely, no strong immobilization has been observed for the GFP, as these molecules were easily displaced by the scanning tip. The contrasting behaviour of the two proteins can be explained by the exposed molecular surface area of their cysteine residues as modelled on the basis of their respective X-ray crystallographic data structures. GFP contains two cysteine residues, but neither is readily available to chemisorb on the gold clusters, because the cysteines are largely inaccessible from the surface of the protein. In contrast, OSM has a total of five cysteine residues, with different degrees of accessibility, which make the protein amenable to anchoring on the nanoclusters. Statistical analysis of the height of the OSM molecules bound to the nanoclusters is in accordance with crystallographic data, and suggests various configurations of the proteins on the clusters, associated with the presence of different cysteine anchoring sites. These results suggest that the three-dimensional conformation of protein molecules is preserved when they are chemisorbed to size-selected gold clusters, thus opening a new route towards oriented immobilization of individual protein molecules.

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing.

Toward direct measurement of atmospheric nucleation.

Atmospheric aerosol formation is known to occur almost all over the world, and the importance of these particles to climate and air quality has been recognized. Although almost all of the processes driving aerosol formation take place below a particle diameter of 3 nanometers, observations cover only larger particles. We introduce an instrumental setup to measure atmospheric concentrations of both neutral and charged nanometer-sized clusters. By applying the instruments in the field, we come to three important conclusions: (i) A pool of numerous neutral clusters in the sub-3 nanometer size range is continuously present; (ii) the processes initiating atmospheric aerosol formation start from particle sizes of approximately 1.5 nanometers; and (iii) neutral nucleation dominates over the ion-induced mechanism, at least in boreal forest conditions.