Taxonomic and environmental distribution of bacterial amino acid auxotrophies.

Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of 'streamlined' life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark.

BACKGROUND: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. METHODS: We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. RESULTS: In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. CONCLUSIONS: Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants.

Utility of optical facial feature and arm movement tracking systems to enable text communication in critically ill patients who cannot otherwise communicate.

PURPOSE: Patients recovering from critical illness especially those with critical illness related neuropathy, myopathy, or burns to face, arms and hands are often unable to communicate by writing, speech (due to tracheostomy) or lip reading. This may frustrate both patient and staff. Two low cost movement tracking systems based around a laptop webcam and a laser/optical gaming system sensor were utilised as control inputs for on-screen text creation software and both were evaluated as communication tools in volunteers. METHODS: Two methods were used to control an on-screen cursor to create short sentences via an on-screen keyboard: (i) webcam-based facial feature tracking, (ii) arm movement tracking by laser/camera gaming sensor and modified software. 16 volunteers with simulated tracheostomy and bandaged arms to simulate communication via gross movements of a burned limb, communicated 3 standard messages using each system (total 48 per system) in random sequence. RESULTS: Ten and 13 minor typographical errors occurred with each system respectively, however all messages were comprehensible. Speed of sentence formation ranged from 58 to 120s with the facial feature tracking system, and 60-160s with the arm movement tracking system. The average speed of sentence formation was 81s (range 58-120) and 104s (range 60-160) for facial feature and arm tracking systems respectively, (P<0.001, 2-tailed independent sample t-test). CONCLUSION: Both devices may be potentially useful communication aids in patients in general and burns critical care units who cannot communicate by conventional means, due to the nature of their injuries.

Estimating and testing haplotype-trait associations in non-diploid populations.

Malaria is an infectious disease that is caused by a group of parasites of the genus Plasmodium. Characterizing the association between polymorphisms in the parasite genome and measured traits in an infected human host may provide insight into disease aetiology and ultimately inform new strategies for improved treatment and prevention. This, however, presents an analytic challenge since individuals are often multiply infected with a variable and unknown number of genetically diverse parasitic strains. In addition, data on the alignment of nucleotides on a single chromosome, which is commonly referred to as haplotypic phase, is not generally observed. An expectation-maximization algorithm for estimating and testing associations between haplotypes and quantitative traits has been described for diploid (human) populations. We extend this method to account for both the uncertainty in haplotypic phase and the variable and unknown number of infections in the malaria setting. Further extensions are described for the human immunodeficiency virus quasi-species setting. A simulation study is presented to characterize performance of the method. Application of this approach to data arising from a cross-sectional study of n=126 multiply infected children in Uganda reveals some interesting associations requiring further investigation.

Mitochondrial DNA variation in Mauritania and Mali and their genetic relationship to other Western Africa populations.

Mitochondrial DNA (mtDNA) variation was analyzed in Mauritania and Mali, and compared to other West African samples covering the considerable geographic, ethnic and linguistic diversity of this region. The Mauritanian mtDNA profile shows that 55% of their lineages have a west Eurasian provenance, with the U6 cluster (17%) being the best represented. Only 6% of the sub-Saharan sequences belong to the L3A haplogroup a frequency similar to other Berber speaking groups but significantly different to the Arabic speaking North Africans. The historic Arab slave trade may be the main cause of this difference. Only one HV west Eurasian lineage has been detected in Mali but 40% of the sub-Saharan sequences belong to cluster L3A. The presence of L0a representatives demonstrates gene flow from eastern regions. Although both groups speak related dialects of the Mande branch, significant genetic differences exist between the Bambara and Malinke groups. The West African genetic variation is well structured by geography and language, but more detailed ethnolinguistic clustering suggest that geography is the main factor responsible for this differentiation.

A complement receptor-1 polymorphism with high frequency in malaria endemic regions of Asia but not Africa.

Complement receptor-1 (CR1) is a ligand for rosette formation, a phenomenon associated with cerebral malaria (CM). Binding is dependent on erythrocyte CR1 copy number. In Caucasians, low CR1 expressors have two linked mutations. We determined the Q981H and HindIII RFLP distribution in differing population groups to ascertain a possible role in adaptive evolution. We examined 194 Caucasians, 180 Choctaw Indians, 93 Chinese-Taiwanese, 304 Cambodians, 89 Papua New Guineans (PNG) and 366 Africans. PCR/RFLP used HindIII for CR1 expression and BstNI for the Q981H mutation. DNA sequencing and pyrosequencing were performed to resolve inconclusive results. Gene frequencies for the L allele were 0.15 in Africans, 0.16 in Choctaws, 0.18 in Caucasians, 0.29 in Chinese-Taiwanese, 0.47 in Cambodians and 0.58 in PNG. Allelic frequency for 981H were 0.07 in Africans, 0.15 in Caucasians, 0.18 in Choctaws, 0.29 in Chinese-Taiwanese, 0.47 in Cambodians and 0.54 in PNG. The Q981H polymorphism correlates with the HindIII RFLP in most groups except West Africans and appears to be part of a low CR1 expression haplotype. The gene frequency for the haplotype is highest in the malaria-endemic areas of Asia, suggesting that this haplotype may have evolved because it protects from rosetting and CM.

Zoonotic infections in Nigeria: overview from a medical perspective.

Infections of domestic and wild animals that are transmitted directly or by an arthropod vector to humans are a major cause of morbidity and mortality worldwide and particularly in Nigeria. With a population of over 100 million and the need for improved health care delivery, Nigerians are at considerable risk considering the seriousness of these infections. Zoonotic infections that are endemic in Nigeria include tuberculosis, trypanosomiasis, toxoplasmosis, taeniasis, rabies, lassa fever and yellow fever. Zoonotic food-borne infections (caused by Campylobacter, Salmonella and Escherichia coli O157:H7) and cryptosporidiosis are emerging. Sporadic cases such as strongyloidiasis, ascariasis, leptospirosis, scabies, pentastomiasis and African histoplasmosis have been reported. There is a need to determine the prevalence of tick-borne zoonoses. Prevention and control of zoonoses in humans is by vaccination, treatment and health education. As a first measure to improve control, the link between veterinary and medical officers, which is presently very weak, needs to be strengthened. Furthermore, regional multidisciplinary approaches to the control of zoonotic infections should be adopted in West Africa, which take into consideration the huge inter-border traffic.

Lipid tubule self-assembly: length dependence on cooling rate through a first-order phase transition.

The formation kinetics and self-assembly of multilamellar tubules of the diacetylenic phospholipid 1,2-bis(tricosa-10,12-diynoyl)-sn-glycerol-3-phosphocholine formed under controlled cooling rates were studied by x-ray diffraction and optical, atomic force, and scanning electron microscopy. Tubule formation was driven by a reversible first-order phase transition from an intralamellar, chain-melted L(alpha) phase to a chain-frozen L(beta), phase. These observations are the basis of a highly efficient method of tubule production in which tubule lengths can be controlled, between 1 and 100 micrometers, by varying the cooling rate. These tubules can be made in suspensions with 10 percent lipid by mass, far exceeding the lipid solubility limit.

Ethanol-induced disordering of membranes from different age groups of C57BL/6NNIA mice.

In previous studies, we have shown that many of the pharmacological effects of ethanol administered in vivo are greater in older mice compared to younger mice. This study determined if there are age-related differences in membrane order when ethanol is administered in vitro. Synaptic plasma membranes, brain microsomal membranes and erythrocyte membranes were isolated from young (3-5 month), middle (11-13 months), and old (22-24 months) C57BL/6NNIA mice. The order parameter of each age group was measured using a 5-nitroxide stearic acid spin label in the presence of 0, 250 and 500 mM ethanol added in vitro. No age-related differences in order parameter were seen in the absence of ethanol. However, membranes from young animals were disordered to the greatest degree by ethanol. The synaptic plasma and erythrocyte membranes from young mice were disordered by both 250 and 500 mM ethanol. Membranes from old mice were disordered significantly by 500 mM ethanol only and the disordering was not as great as was seen in the membranes from the young mice. In the microsomal membrane preparation, 500 mM ethanol significantly disordered the membranes from the young animals, but it had no effect on membranes from old animals. Age differences were also observed generally for cholesterol and total phospholipid which both increased with increasing age for synaptic plasma and brain microsomes. Membrane disorder induced by ethanol differs with age and is associated with cholesterol and phospholipid content of membranes.