Thanks to the Cassini-Huygens space mission between 2004 and 2017, a lot was learned about Titan, the biggest satellite of Saturn, and its intriguing atmosphere, surface, and organic chemistry ...complexity. However, key questions about the potential for the atmosphere and surface chemistry to produce organic molecules of direct interest for prebiotic chemistry and life did not find an answer. Due to Titan potential as a habitable world, NASA selected the Dragonfly space mission to be launched in 2027 to Titan's surface and explore the Shangri-La surface region for minimum 3 years. One of the main goals of this mission will be to understand the past and actual abundant prebiotic chemistry on Titan, especially using the Dragonfly Mass Spectrometer (DraMS). Two recently used sample pre-treatments for Gas Chromatography – Mass Spectrometry (GC-MS mode of DraMS) analyses are planned prior analysis to extract refractory organic molecules of interest for prebiotic chemistry and astrobiology. The dimethylformamide dimethylacetal (DMF-DMA) derivatization reaction offers undoubtedly an opportunity to detect biosignatures by volatilizing refractory biological or prebiotic molecules and conserving the chiral carbons’ conformation while an enantiomeric excess indicates a chemical feature induced primarily by life (and may be aided on the primitive systems by light polarization). The goal of this study is to investigate the ageing of DMF-DMA in DraMS (and likely MOMA) capsules prior to in situ analysis on Titan (or Mars). The main results highlighted by our work on DMF-DMA are first its satisfactory stability for space requirements through time (no significant degradation over a year of storage and less than 30% of lost under thermal stress) to a wide range of temperature (0°C to 250°C), or the presence of water and oxidants during the derivatization reaction (between 0 and 10% of DMF-DMA degradation). Moreover, this reagent derivatized very well amines and carboxylic acids in high or trace amounts (ppt to hundreds of ppm), conserving their molecular conformation during the heat at 145°C for 3 minutes (0 to 4 % in the enantiomeric form change).
•DMF-DMA fast one-pot derivatization reaction on polar and refractory molecules.•DMF-DMA enables the molecules’ chiral center configuration to be safely preserved.•Amino acids derivatized by DMF-DMA ...were analyzed by GC–MS down to a few ppt-ppb.•More than 70 % of DMF-DMA in space capsules will be preserved from space conditions.•DMF-DMA is slightly sensitive to oxidants and temperature (10 % of degradation).
Thanks to the Cassini-Huygens space mission between 2004 and 2017, a lot was learned about Titan, the biggest satellite of Saturn, and its intriguing atmosphere, surface, and organic chemistry complexity. However, key questions about the potential for the atmosphere and surface chemistry to produce organic molecules of direct interest for prebiotic chemistry and life did not find an answer. Due to Titan potential as a habitable world, NASA selected the Dragonfly space mission to be launched in 2027 to Titan's surface and explore the Shangri-La surface region for minimum 3 years. One of the main goals of this mission will be to understand the past and actual abundant prebiotic chemistry on Titan, especially using the Dragonfly Mass Spectrometer (DraMS). Two recently used sample pre-treatments for Gas Chromatography – Mass Spectrometry (GC–MS mode of DraMS) analyses are planned prior analysis to extract refractory organic molecules of interest for prebiotic chemistry and astrobiology. The dimethylformamide dimethylacetal (DMF-DMA) derivatization reaction offers undoubtedly an opportunity to detect biosignatures by volatilizing refractory biological or prebiotic molecules and conserving the chiral carbons’ conformation while an enantiomeric excess indicates a chemical feature induced primarily by life (and may be aided on the primitive systems by light polarization). The goal of this study is to investigate the ageing of DMF-DMA in DraMS (and likely MOMA) capsules prior to in situ analysis on Titan (or Mars). The main results highlighted by our work on DMF-DMA are first its satisfactory stability for space requirements through time (no significant degradation over a year of storage and less than 30 % of lost under thermal stress) to a wide range of temperature (0 °C to 250 °C), or the presence of water and oxidants during the derivatization reaction (between 0 and 10 % of DMF-DMA degradation). Moreover, this reagent derivatized very well amines and carboxylic acids in high or trace amounts (ppt to hundreds of ppm), conserving their molecular conformation during the heat at 145 °C for 3 min (0 to 4% in the enantiomeric form change).
A straight, non-sporulating, Gram-variable bacillus （HKU24^T） was recovered from the blood culture of a patient with metastatic breast carcinoma. After repeated subculturing in BACTEC Plus ...Anaerobic/F blood culture broth, HKU24T grew on brucella agar as non-hemolytic, pinpoint colonies after 96 h of incubation at 37 °C in an anaerobic environment and aerobic environment with 5% CO2. Growth was enhanced with a streak of Staphylococcus aureus. HKU24^T was non-motile and catalase-negative, but positive for alkaline phosphatase, β-glucosidase, and α-glucosidase. It hydrolyzed phenylphosphonate and reduced resazurin. 16S rRNA, groEL, gyrB, recA, and rpoB sequencing showed that HKU24^T occupies a distinct phylogenetic position among the Leptotrichia species, being most closely related to Leptotrichia trevisanii. Using HKU24^T groEL, gyrB, recA, and rpoB gene-specific primers, fragments of these genes were amplified from one of 20 oral specimens. Based on phenotypic and genotypic characteristics, we propose a new species, Leptotrichia hongkongensis sp. nov., to describe this bacterium.
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data ...alone to completely sequence a two-chromosome bacterial genome from a single library in a single run. Previous studies using earlier versions of sequencing chemistries have at most been able to finish bacterial genomes containing only one chromosome with
assembly. In this study, we compared the robustness of PacBio RS II, using one SMRT cell and the latest P6-C4 chemistry, with Illumina HiSeq 1500 in sequencing the genome of
, a bacterium which contains two large circular chromosomes, very high G+C content of 68-69%, highly repetitive regions and substantial genomic diversity, and represents one of the largest and most complex bacterial genomes sequenced, using a reference genome generated by hybrid assembly using PacBio and Illumina datasets with subsequent manual validation. Results showed that PacBio data with
assembly, but not Illumina, was able to completely sequence the
genome without any gaps or mis-assemblies. The two large contigs of the PacBio assembly aligned unambiguously to the reference genome, sharing >99.9% nucleotide identities. Conversely, Illumina data assembled using three different assemblers resulted in fragmented assemblies (201-366 contigs), sharing only 92.2-100% and 92.0-100% nucleotide identities to chromosomes I and II reference sequences, respectively, with no indication that the
genome consisted of two chromosomes with four copies of ribosomal operons. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing (wgMLST). Most notably, assembly solely based on PacBio outperformed even hybrid assembly using both PacBio and Illumina datasets. Hybrid approach generated only 74 contigs, while the PacBio data alone with
assembly achieved complete closure of the two-chromosome
genome without additional costly bench work and further sequencing. PacBio RS II using P6-C4 chemistry is highly robust and cost-effective and should be the platform of choice in sequencing bacterial genomes, particularly for those that are well-known to be difficult-to-sequence.
The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as ...vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.
Three bacterial strains, HKU70
, HKU71
and HKU72
, were isolated from the conjunctival swab, blood and sputum samples of three patients with conjunctivitis, bacteraemia and respiratory infection, ...respectively, in Hong Kong. The three strains were aerobic, Gram-stain positive, catalase-positive, non-sporulating and non-motile bacilli and exhibited unique biochemical profiles distinguishable from currently recognized
species. 16S rRNA,
,
and
gene sequence analyses revealed that the three strains shared 99.6-99.9, 94.5-96.8, 95.7-97.8 and 97.7-98.9 % nucleotide identities with their corresponding closest
species respectively. DNA-DNA hybridization confirmed that they were distinct from other known species of the genus
(26.2±2.4 to 36.8±1.2 % DNA-DNA relatedness), in line with results of
genome-to-genome comparison (32.2-40.9 % Genome-to-Genome Distance Calculator and 86.3-88.9 % average nucleotide identity values. Fatty acids, mycolic acids, cell-wall sugars and peptidoglycan analyses showed that they were typical of members of
. The G+C content determined based on the genome sequence of strains HKU70
, HKU71
and HKU72
were 69.9, 70.2 and 70.5 mol%, respectively. Taken together, our results supported the proposition and description of three new species, i.e.
HKU70
(=JCM 33387
=DSM 109106
) sp. nov.,
HKU71
(=JCM 33388
=DSM 109107
) sp. nov. and
HKU72
(=JCM 33389
=DSM 109108
) sp. nov.
Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75
, in pure culture ...from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75
was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75
was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75
was unidentifiable. MALDI-TOF MS identified HKU75
as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75
was most closely related to
(98.3% nucleotide identity), whereas partial
and
gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75
and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75
belonged to the Suis group.
gene sequences identical to that of HKU75
could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75
is a novel Streptococcus species, which we propose to be named
. The oral cavity of guinea pigs is presumably a reservoir of
. Some of the reported S. suis strains isolated from clinical specimens may be
.
We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/
by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that
belongs to the Suis group.
sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of
. Some of the reported S. suis strains may be
. Further studies are warranted to refine our knowledge on this novel Streptococcus species.
The newly described brittle tail syndrome causes weakening and breakage of the tail hair of horses. Extensive mycological and molecular studies showed that a novel fungus Equicapillimyces ...hongkongensis gen. nov., sp. nov. is the most likely cause of this syndrome. It is a septate branching hyaline mould which grows optimally at 30°C, requires nicotinic acid but is inhibited by cycloheximide, and specifically infects horse hair. Hyphae fill the core of infected hair shafts with short-necked structures resembling ascomata containing banana-shaped septate ascospore-like structures perforating the hair cortex from within. Compared to asymptomatic horses (n=31), horses with clinical signs of the syndrome (n=22) are significantly more likely to have positive E. hongkongensis gen. nov., sp. nov. smear (6.5% vs. 100%), culture (6.5% vs. 72.7%), and PCR (32.3% vs. 100%, P<0.001 for all). No other potential pathogens were found on bacteriological and mycological culture or PCR (for Trichophyton, Microsporum and Epidermophyton). Genotyping of pure E. hongkongensis gen. nov., sp. nov. isolates and their corresponding direct specimens by PCR and sequencing of the 18S rRNA, ITS1–5.8S-ITS2, 28S rRNA, beta-actin, beta-tubulin, and elongation factor 1 alpha showed that they are all identical but unique, and related distantly to fungi mostly in the class Sordariomycetes and the family Ophiostomataceae. Its geographical distribution, environmental or animal reservoirs are still unknown. Besides the ugly appearance of infected horse tails, this fungus may emerge as another equine pathogen if it affects the skin and hoof of horses.
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