Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes

The generation of microarray probes with specificity below the species level is an ongoing challenge, not least because the high-throughput detection of microorganisms would be an efficient means of identifying environmentally relevant microbes. Here, we describe how suppression subtractive hybridization (SSH) can be applied to the production of microarray probes that are useful for microbial differentiation at the subspecies level. SSH was used to initially isolate unique genomic sequences of nine Salmonella strains, and these were validated in quadruplicate by microarray analysis. The results obtained indicate that a large group of genes subtracted by SSH could serve together, as one probe, for detecting a microbial subspecies. Similarly, the whole microbial genome (not subjected to SSH) can be used as a species-specific probe. The detailed methods described herein could be used and adapted for the estimation of any cultivable bacteria from different environments

Physical and electrochemical properties of synthesized carbon nanotubes [CNTs] on a metal substrate by thermal chemical vapor deposition

Multi-walled carbon nanotubes were synthesized on a Ni/Au/Ti substrate using a thermal chemical vapor deposition process. A Ni layer was used as a catalyst, and an Au layer was applied as a barrier in order to prevent diffusion between Ni and Ti within the substrate during the growth of carbon nanotubes. The results showed that vertically aligned multi-walled carbon nanotubes could be uniformly grown on the Ti substrate (i.e., metal substrate), thus indicating that the Au buffer layer effectively prevented interdiffusion of the catalyst and metal substrate. Synthesized carbon nanotubes on the Ti substrate have the diameter of about 80 to 120 nm and the length of about 5 to 10 μm. The Ti substrate, with carbon nanotubes, was prepared as an electrode for a lithium rechargeable battery, and its electrochemical properties were investigated. In a Li/CNT cell with carbon nanotubes on a 60-nm Au buffer layer, the first discharge capacity and discharge capacity after the 50th cycle were 210 and 80 μAh/cm2, respectively

Subacute Neurological Deterioration with Selective Axonal Injury in Patients with Acute Ischemic Stroke following Reperfusion of Middle Cerebral Artery Occlusion

To date, the long-term effects of reperfusion on the salvaged brain tissues have not been addressed in the literature. We report 4 cases presenting subacute neurological deteriorations with selective axonal injury following reperfusion therapies for acute ischemic stroke. Our case series based on 4 patients showed common features distinct from those of early reperfusion injury in that (1) the neurological symptoms developed after 1-2 months of reperfusion therapies, (2) these symptoms were accompanied by the subcortical white matter changes on brain MRI, and (3) these findings were mostly reversible with time. This suggests that axons in the reperfused brain may be vulnerable to further neurological injury

Analysis of speech and tongue motion in normal and post-glossectomy speaker using cine MRI

Objective Since the tongue is the oral structure responsible for mastication, pronunciation, and swallowing functions, patients who undergo glossectomy can be affected in various aspects of these functions. The vowel /i/ uses the tongue shape, whereas /u/ uses tongue and lip shapes. The purpose of this study is to investigate the morphological changes of the tongue and the adaptation of pronunciation using cine MRI for speech of patients who undergo glossectomy. Material and Methods Twenty-three controls (11 males and 12 females) and 13 patients (eight males and five females) volunteered to participate in the experiment. The patients underwent glossectomy surgery for T1 or T2 lateral lingual tumors. The speech tasks “a souk” and “a geese” were spoken by all subjects providing data for the vowels /u/ and /i/. Cine MRI and speech acoustics were recorded and measured to compare the changes in the tongue with vowel acoustics after surgery. 2D measurements were made of the interlip distance, tongue-palate distance, tongue position (anterior-posterior and superior-inferior), tongue height on the left and right sides, and pharynx size. Vowel formants Fl, F2, and F3 were measured. Results The patients had significantly lower F2/Fl ratios (F=5.911, p=0.018), and lower F3/F1 ratios that approached significance. This was seen primarily in the /u/ data. Patients had flatter tongue shapes than controls with a greater effect seen in /u/ than /i/. Conclusion The patients showed complex adaptation motion in order to preserve the acoustic integrity of the vowels, and the tongue modified cavity size relationships to maintain the value of the formant frequencies

Composition and source identification of polycyclic aromatic hydrocarbons in mangrove sediments of Peninsular Malaysia : indication of anthropogenic input.

This is a comprehensive study of the composition, origin and sources of specific polycyclic aromatic hydrocarbons (PAHs) in sediments of mangrove estuary in the western part of Peninsular Malaysia. Mangrove sediments were analyzed for 17 PAHs by gas chromatography–mass spectrometry. Total PAH concentrations in the sediments ranged from 20 to 112 ng/g on a dry-weight basis. High molecular weight PAHs were abundant in the sediments. Parent PAH ratios revealed that pyrogenic input has important contribution to the sedimentary PAHs. Ratios of alkylated PAHs indicate that the sedimentary PAHs were influenced by petrogenic PAHs, which implies that petrogenic input has contribution to the sedimentary PAHs but that it is not a major factor in distribution of PAHs within the estuary. Combustion-derived PAHs show a positive and very strong correlation with total PAHs (R 2 = 0.926, p < 0.05). Total methylphenanthrenes show very weak correlation with total PAHs (R 2 = 0.0928, p < 0.05). The PAH concentrations were found to increase with distance from the upstream of the estuary to the coastal area of the Straits of Malacca. For the assessment of sediment contamination using biological thresholds, none of the individual studied PAH compounds exceeded the values of the effect range low–effect range median guideline and the threshold effects level–probable effects level guideline. This study demonstrates that the sediments of the mangrove ecosystem facing the Straits of Malacca and Sumatra are influenced by anthropogenic PAH inputs as a result of human activities such as biomass burning, vehicle emissions and boating activities

Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota.

Daily PrEP is highly effective at preventing HIV-1 acquisition, but risks of long-term tenofovir disoproxil fumarate plus emtricitabine (TDF-FTC) include renal decline and bone mineral density decrease in addition to initial gastrointestinal side effects. We investigated the impact of TDF-FTC on the enteric microbiome using rectal swabs collected from healthy MSM before PrEP initiation and after 48 to 72 weeks of adherent PrEP use. The V4 region of the 16S ribosomal RNA gene sequencing showed that Streptococcus was significantly reduced from 12.0% to 1.2% (p = 0.036) and Erysipelotrichaceae family was significantly increased from 0.79% to 3.3% (p = 0.028) after 48-72 weeks of daily PrEP. Catenibacterium mitsuokai, Holdemanella biformis and Turicibacter sanguinis were increased within the Erysipelotrichaceae family and Streptococcus agalactiae, Streptococcus oralis, Streptococcus mitis were reduced. These changes were not associated with host factors including PrEP duration, age, race, tenofovir diphosphate blood level, any drug use and drug abuse, suggesting that the observed microbiome shifts were likely induced by daily PrEP use. Long-term PrEP resulted in increases of Catenibacterium mitsuokai and Holdemanella biformis, which have been associated with gut microbiome dysbiosis. Our observations can aid in characterizing PrEP's side effects, which is likely to improve PrEP adherence, and thus HIV-1 prevention

The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.

HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. HIV incidence assay performance is evaluated via false recency rate (FRR) and mean duration of recent infection (MDRI). We conducted a meta-analysis of 438 incident and 305 chronic specimens' HIV envelope genes from a diverse global cohort. The genome similarity index (GSI) accurately characterized infection stage across diverse host and viral factors. All except one chronic specimen had GSIs below 0.67, yielding a FRR of 0.33 [0-0.98] %. We modeled the incidence assay biomarker dynamics with a logistic link function assuming individual variabilities in a Beta distribution. The GSI probability density function peaked close to 1 in early infection and 0 around two years post infection, yielding MDRI of 420 [361, 467] days. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 21 subjects who followed from HIV negative status. Both standardized residuals and Anderson-Darling tests showed that the test dataset was statistically consistent with the model biomarker dynamics. This is the first reported incidence assay meeting the optimal FRR and MDRI performance standards. Signatures of HIV gene diversification can allow precise cross-sectional surveillance with a desirable temporal range of incidence detection

One-step fabrication of surface-decorated inorganic nanowires via single-nozzle electrospinning

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1A6A3A03004416) and (NRF-2015M1A2A2056833).One-dimensional heterostructured nanomaterials represent key building blocks for nanotechnologies due to a large number of applications such as electronics, catalysis, drug delivery, and energy storage and conversion devices. Electrospinning has been considered a straightforward and versatile method to prepare inorganic nanowires, but the heterostructured nanowires have been only fabricated by using dual-nozzle or by introducing additional encapsulating step. Here we report one-step fabrication of surface-decorated inorganic nanowires via single-nozzle electrospinning. Although the electrospinning precursor uses one mixed solution containing nickel salt, ceria nanoparticles, and polyvinylpyrrolidine (PVP), the nanowires show a core/shell-like shape. The surface-decorated nanowires consist of nickel shell and ceria core, which exhibits 95.52% of methane conversion at 600 °C whereas conventional particle-type catalysts have only 60% at the same temperature in steam reforming.PostprintPeer reviewe

1-(2-Hy­droxy­eth­yl)-3-(3-meth­oxy­phen­yl)thio­urea

In the title compound, C10H14N2O3S, the 3-meth­oxy­phenyl unit is almost planar, with an r.m.s. deviation of 0.013 Å. The dihedral angle between the benzene ring and the plane of the thio­urea unit is 62.57 (4)°. In the crystal, N—H⋯O and O—H⋯S hydrogen bonds link the mol­ecules into a three-dimensional network

1-(4-Hy­droxy­phen­yl)-3-(3,4,5-tri­methoxy­phen­yl)thio­urea

In the title compound, C16H18N2O4S, the dihedral angle between the hy­droxy­phenyl ring and the plane of the thio­urea moiety is 54.53 (8)°. The H atoms of the NH groups of thio­urea are positioned anti to each other. In the crystal, inter­molecular N—H⋯S, N—H⋯O, and O—H⋯S hydrogen bonds link the mol­ecules into a three-dimensional network