ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication

The β-coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the global Covid-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release and pathogenesis. We developed a non-disruptive tagging strategy for SARS-CoV-2 E and find that at steady-state, it localises to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for Endoplasmic Reticulum (ER)-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP Ribosylation Factor-1/Adaptor Protein-1 (ARFRP1/AP-1) dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and by developing a trans-complementation assay for SARS-CoV-2 structural proteins, we show that lysosomal delivery of E and its viroporin activity are necessary for efficient viral replication and release

Pyroclastic Deposits in Floor-Fractured Craters: A Unique Style or Lunar Basaltic Volcanism?

The lunar maria were formed by effusive fissure flows of low-viscosity basalt. Regional pyroclastic deposits were formed by deep-sourced fire-fountain eruptions dominated by basaltic glass. Basaltic material is also erupted from small vents within floor-fractured impact craters. These craters are characterized by shallow, flat floors cut by radial, concentric and/or polygonal fractures. Schultz [1] identified and classified over 200 examples. Low albedo pyroclastic deposits originate from depressions along the fractures in many of these craters

Pyroclastic Deposits in the Floor-fractured Crater Alphonsus

Alphonsus, the 118 km diameter floor-fractured crater, is located immediately east of Mare Nubium. Eleven pyroclastic deposits have been identified on the crater's floor. Early telescopic spectra suggest that the floor of Alphonsus is noritic, and that the pyroclastic deposits contain mixtures of floor material and a juvenile component including basaltic glass. Head and Wilson contend that Nubium lavas intruded the breccia zone beneath Alphonsus, forming dikes and fractures on the crater floor. In this model, the magma ascended to the level of the mare but cooled underground, and a portion broke thru to the surface in vulcanian (explosive) eruptions. Alternatively, the erupted material could be from a source unrelated to the mare, in the style of regional pyroclastic deposits. High-resolution images and spectroscopy from the Moon Mineralogy Mapper (M3), Diviner Lunar Radiometer, and Lunar Reconnaissance Orbiter Camera Narrow Angle Camera (NAC) provide data to test these formation models. Spectra from M3 confirm that the crater floor is primarily composed of noritic material, and that the Nubium lavas are basaltic. Spectra from the three largest pyroclastic deposits in Alphonsus are consistent with a minor low- Ca pyroxene component in a glass-rich matrix. The centers of the 2 micron absorption bands have wavelengths too short to be of the same origin as the Nubium basalts. Diviner Christiansen feature (CF) values were used to estimate FeO abundances for the crater floor, Nubium soil, and pyroclastic deposits. The estimated abundance for the crater floor (7.5 +/- 1.4 wt.%) is within the range of FeO values for Apollo norite samples. However, the estimated FeO abundance for Nubium soil (13.4 +/- 1.4 wt.%) is lower than those measured in most mare samples. The difference may reflect contamination of the mare soil by highland ejecta. The Diviner-derived FeO abundance for the western pyroclastic deposit is 13.8 +/- 3.3 wt.%. This is lower than the values for mare soil samples, but within the range of analyzed pyroclastic glasses. The NAC images of the pyroclastic vents highlight their bright wall materials. The M3 spectra of the southeastern vent indicate that this bright material is noritic, likely crater floor material exposed by explosive eruption. These observations address the hypothesis that Nubium lavas intruded the fracture network beneath Alphonsus, leading to localized vulcanian-style eruptions. This model implies that the eruption products should be dominated by crystalline basalt fragments similar in elemental composition and mineralogy to mare lavas. The bright noritic material exposed in the vent walls is consistent with explosive eruptions. The estimated FeO abundances for the pyroclastic deposits are too low to be consistent with FeO abundances measured in mare basalts, but are within the range of pyroclastic glass samples. The visible- to near-infrared (VIS-NIR) spectra of the pyroclastic deposits and Nubium soils are significantly different, suggesting that the pyroclastics are unrelated to the mare basalts. The pyroclastic spectra are consistent with Fe-bearing glass plus small amounts of noritic wall rock. Similar glassy materials dominate regional pyroclastic deposits, suggesting a deep source for the pyroclastics observed in Alphonsus

Preliminary genetic evidence of two different populations of Opisthorchis viverrini in Lao PDR

Opisthorchis viverrini is a major public health concern in Southeast Asia. Various reports have suggested that this parasite may represent a species complex, with genetic structure in the region perhaps being dictated by geographical factors and different species of intermediate hosts. We used four microsatellite loci to analyze O. viverrini adult worms originating from six species of cyprinid fish in Thailand and Lao PDR. Two distinct O. viverrini populations were observed. In Ban Phai, Thailand, only one subgroup occurred, hosted by two different fish species. Both subgroups occurred in fish from That Luang, Lao PDR, but were represented to very different degrees among the fish hosts there. Our data suggest that, although geographical separation is more important than fish host specificity in influencing genetic structure, it is possible that two species of Opisthorchis, with little interbreeding, are present near Vientiane in Lao PDR

Trends in Caffeine Use and Association between Clinical Outcomes and Timing of Therapy in Very Low Birth Weight Infants

Objective: To examine the effect of early initiation of caffeine therapy on neonatal outcomes and characterize the use of caffeine therapy in very low birth weight (VLBW) infants. Study design: We analyzed a cohort of 62 056 VLBW infants discharged between 1997 and 2010 who received caffeine therapy. We compared outcomes in infants receiving early caffeine therapy (initial dose before 3 days of life) and those receiving late caffeine therapy (initial dose at or after 3 days of life) through propensity scoring using baseline and early clinical variables. The primary outcome was the association between the timing of caffeine initiation and the incidence of bronchopulmonary dysplasia (BPD) or death. Results: We propensity score–matched 29 070 VLBW infants at a 1:1. Of infants receiving early caffeine therapy, 3681 (27.6%) died or developed BPD, compared with 4591 infants (34.0%) receiving late caffeine therapy (OR, 0.74; 99% CI, 0.69-0.80). Infants receiving early caffeine had a lower incidence of BPD (23.1% vs 30.7%; OR, 0.68; 95% CI, 0.63-0.73) and a higher incidence of death (4.5% vs 3.7%; OR, 1.23; 95% CI, 1.05-1.43). Infants receiving early caffeine therapy had less treatment of patent ductus arteriosus (OR, 0.60; 95% CI, 0.55-0.65) and a shorter duration of mechanical ventilation (mean difference, 6 days; P \u3c .001). Conclusion: Early caffeine initiation is associated with a decreased incidence of BPD. Randomized trials are needed to determine the efficacy and safety of early caffeine prophylaxis in VLBW infants. (J Pediatr 2014; 164:992-8)

Trends in Caffeine Use and Association between Clinical Outcomes and Timing of Therapy in Very Low Birth Weight Infants

Objective: To examine the effect of early initiation of caffeine therapy on neonatal outcomes and characterize the use of caffeine therapy in very low birth weight (VLBW) infants. Study design: We analyzed a cohort of 62 056 VLBW infants discharged between 1997 and 2010 who received caffeine therapy. We compared outcomes in infants receiving early caffeine therapy (initial dose before 3 days of life) and those receiving late caffeine therapy (initial dose at or after 3 days of life) through propensity scoring using baseline and early clinical variables. The primary outcome was the association between the timing of caffeine initiation and the incidence of bronchopulmonary dysplasia (BPD) or death. Results: We propensity score–matched 29 070 VLBW infants at a 1:1. Of infants receiving early caffeine therapy, 3681 (27.6%) died or developed BPD, compared with 4591 infants (34.0%) receiving late caffeine therapy (OR, 0.74; 99% CI, 0.69-0.80). Infants receiving early caffeine had a lower incidence of BPD (23.1% vs 30.7%; OR, 0.68; 95% CI, 0.63-0.73) and a higher incidence of death (4.5% vs 3.7%; OR, 1.23; 95% CI, 1.05-1.43). Infants receiving early caffeine therapy had less treatment of patent ductus arteriosus (OR, 0.60; 95% CI, 0.55-0.65) and a shorter duration of mechanical ventilation (mean difference, 6 days; P \u3c .001). Conclusion: Early caffeine initiation is associated with a decreased incidence of BPD. Randomized trials are needed to determine the efficacy and safety of early caffeine prophylaxis in VLBW infants. (J Pediatr 2014; 164:992-8)

The genome sequence of <i>Trypanosoma brucei gambiense</i>, causative agent of chronic Human African Trypanosomiasis

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; &lt;i&gt;Trypanosoma brucei gambiense&lt;/i&gt; is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a &lt;i&gt;T. b. brucei&lt;/i&gt; isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between &lt;i&gt;T. b. gambiense&lt;/i&gt; and the reference genome. We sought to identify features that were uniquely associated with &lt;i&gt;T. b. gambiense&lt;/i&gt; and its ability to infect humans.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and findings:&lt;/b&gt; An improved high-quality draft genome sequence for the group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with &lt;i&gt;T. b. brucei&lt;/i&gt; showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972. A comparison of the variant surface glycoproteins (VSG) in &lt;i&gt;T. b. brucei&lt;/i&gt; with all &lt;i&gt;T. b. gambiense&lt;/i&gt; sequence reads showed that the essential structural repertoire of VSG domains is conserved across &lt;i&gt;T. brucei&lt;/i&gt;.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study provides the first estimate of intraspecific genomic variation within &lt;i&gt;T. brucei&lt;/i&gt;, and so has important consequences for future population genomics studies. We have shown that the &lt;i&gt;T. b. gambiense&lt;/i&gt; genome corresponds closely with the reference, which should therefore be an effective scaffold for any &lt;i&gt;T. brucei&lt;/i&gt; genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in &lt;i&gt;T. b. brucei&lt;/i&gt;, no &lt;i&gt;T. b. gambiense&lt;/i&gt;-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.&lt;/p&gt

Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research.

The study of the three protagonists in malaria-the Plasmodium parasite, the Anopheles mosquito, and the human host-is key to developing methods to control and eventually eliminate the disease. Genomic technologies, including the recent development of next-generation sequencing, enable interrogation of this triangle to an unprecedented level of scrutiny, and promise exciting progress toward real-time epidemiology studies and the study of evolutionary adaptation. We discuss the use of genomics by the International Centers of Excellence for Malaria Research, a network of field sites and laboratories in malaria-endemic countries that undertake cutting-edge research, training, and technology transfer in malarious countries of the world