Exploring the faecal microbiome associated with preterm birth

Jacob Westaway investigated the gut microbiome of preterm infants born in North Queensland, Australia. He observed unique associations between the gut microbiome and the unfavourable covariates, as well as acute modulation in association with probiotic prophylaxis. This supports expansion of the probiotic supplementation criteria and highlights the importance of the microbiome in health

Subgenomic replicons of the flavivirus Kunjin: construction and applications

Several Kunjin virus (KUN) subgenomic replicons containing large deletions in the structural region (C-prM-E) and in the 3' untranslated region (3'UTR) of the genome have been constructed. Replicon RNA Delta ME with 1,987 nucleotides deleted (from nucleotide 417 [in codon 108] in the C gene to nucleotide 2403 near the carboxy terminus of the E gene, inclusive) and replicon RNA C20rep with 2,247 nucleotides deleted (from nucleotide 157 [in codon 20] in C to nucleotide 2403) replicated efficiently in electroporated BHK21 cells. A further deletion from C20rep of 53 nucleotides, reducing the coding sequence in core protein to two codons (C2rep RNA), resulted in abolishment of RNA replication. Replicon Delta ME/76 with a deletion of 76 nucleotides in the 3'UTR of Delta ME RNA (nucleotides 10423 to 10498) replicated efficiently, whereas replicon Delta ME/352 with a larger deletion of 352 nucleotides (nucleotides 10423 to 10774), including two conserved sequences RCS3 and CS3, was significantly inhibited in RNA replication. To explore the possibility of using a reporter gene assay to monitor synthesis of the positive strand and the negative strand of KUN RNA, we inserted a chloramphenicol acetyltransferase (CAT) gene into the 3'UTR of Delta ME/76 RNA under control of the internal ribosomal entry site (IRES) of encephalomyelocarditis virus RNA in both plus (Delta ME/76CAT[+])- and minus (Delta ME/76CAT[-])-sense orientations. Although insertion of the IRES-CAT cassette in the plus-sense orientation resulted in a significant (10- to 20-fold) reduction of RNA replication compared to that of the parental Delta ME/76 RNA, CAT expression was readily detected in electroporated BHK cells. No CAT expression was detected after electroporation of RNA containing the IRES-CAT cassette inserted in the minus-sense orientation despite its apparently more efficient replication (similar to that of Delta ME/76 RNA); this result indicated that KUN negative-strand RNA was probably not released from its template after synthesis. Replacement of the CAT gene in the Delta ME/76CAT(+) RNA with the neomycin gene (Neo) enabled selection and recovery of a BHK cell culture in which the majority of cells were continuously expressing the replicon RNA for 41 days (nine passages) without apparent cytopathic effect. The constructed KUN replicons should provide valuable tools to study flavivirus RNA replication as well as providing possible vectors for a long-lasting and noncytopathic RNA virus expression system

trans-complementation analysis of the flavivirus Kunjin ns5 gene reveals an essential role for translation of its N-terminal half in RNA replication

Recently we described rescue of defective Kunjin virus (KUN) RNAs with small deletions in the methyltransferase and RNA polymerase motifs of the ns5 gene, using BHK cells stably expressing KUN replicon RNA (repBHK cells) as helper (A. A. Khromykh et al., J. Virol. 72:7270-7279, 1998). We have now extended our previous observations and report successful trans-complementation of defective KUN RNAs with most of the ns5 gene deleted or substituted with a heterologous (dengue virus) ns5 sequence. Replication of full-length KUN RNAs with 3'-terminal deletions of 136 (5%), 933 (34%), and 1526 (56%) nucleotides in the ns5 gene was complemented efficiently in transfected repBHK cells. RNA with a larger deletion of 2,042 nucleotides (75%) was complemented less efficiently, and RNA with an even larger deletion of 2,279 nucleotides (84%) was not complemented at all. Chimeric KUN genomic RNA containing 87% of the KUN ns5 gene replaced by the corresponding sequence of the dengue virus type 2 ns5 gene was unable to replicate in normal BHK cells but was complemented in repBHK cells. These results demonstrate for the first time complementation of flavivirus RNAs with large deletions (as much as 75%) in the RNA polymerase gene and establish that translation of most of the N-terminal half of NS5 is essential for complementation in trans. A model of formation of the flavivirus replication complex implicating a possible role in RNA replication of conserved coding sequences in the N-terminal half of NS5 is proposed based on the complementation and earlier results with KUN and on reported data with other flaviviruses

River terrace development in the NE Mediterranean region (Syria and Turkey): Patterns in relation to crustal type

It is widely recognized that the optimal development of river terraces globally has been in the temperate latitudes, with NW and Central Europe being areas of particular importance for the preservation of such archives of Quaternary environmental change. There is also a growing consensus that the principal drivers of terrace formation have been climatic fluctuation against a background of progressive (but variable) uplift. Nonetheless river terraces are widely preserved in the Mediterranean region, where they have often been attributed to the effects of neotectonic activity, with a continuing debate about the relative significance of fluctuating temperature (glacials–interglacials) and precipitation (pluvials–interpluvials). Research in Syria and southern–central Turkey (specifically in the valleys of the Tigris and Ceyhan in Turkey, the Kebir in Syria and the trans-border rivers Orontes and Euphrates) has underlined the importance of uplift rates in dictating the preservation pattern of fluvial archives and has revealed different patterns that can be related to crustal type. The NE Mediterranean coastal region has experienced unusually rapid uplift in the Late Quaternary. The relation between the Kebir terraces and the staircase of interglacial raised beaches preserved along the Mediterranean coastline of NW Syria reinforces previous conclusions that the emplacement of the fluvial terrace deposits in the Mediterranean has occurred during colder climatic episodes

Drainage evolution in the Polish Sudeten Foreland in the context of European fluvial archives

Detailed study of subsurface deposits in the Polish Sudeten Foreland, particularly with reference to provenance data, has revealed that an extensive preglacial drainage system developed there in the Pliocene–Early Pleistocene, with both similarities and differences in comparison with the present-day Odra (Oder) system. This foreland is at the northern edge of an intensely deformed upland, metamorphosed during the Variscan orogeny, with faulted horsts and grabens reactivated in the Late Cenozoic. The main arm of preglacial drainage of this area, at least until the early Middle Pleistocene, was the Palaeo–Nysa Kłodzka, precursor of the Odra left-bank tributary of that name. Significant preglacial evolution of this drainage system can be demonstrated, including incision into the landscape, prior to its disruption by glaciation in the Elsterian (Sanian) and again in the early Saalian (Odranian), which resulted in burial of the preglacial fluvial archives by glacial and fluvioglacial deposits. No later ice sheets reached the area, in which the modern drainage pattern became established, the rivers incising afresh into the landscape and forming post-Saalian terrace systems. Issues of compatibility of this record with the progressive uplift implicit in the formation of conventional terrace systems are examined, with particular reference to crustal properties, which are shown to have had an important influence on landscape and drainage evolution in the region

Location of the River Euphrates in the Late Miocene; dating of terrace gravel at Shireen, Syria

International audienceWe report gravel of the River Euphrates, capped by basalt that is Ar-Ar dated to ~9 Ma, at Shireen in northern Syria. This gravel, preserved by the erosion-resistant basalt, allows us for the first time to reconstruct the history of this major river during the Late Miocene. In response to progressive regional surface uplift, the Euphrates extended SE by ~800 km between the early Middle Miocene, when the coast was near Kahramanmara? in southern Turkey, and the Pliocene, when it lay in western Iraq, east of the Arabian Platform uplands

Digital droplet PCR-based environmental DNA tool for monitoring Cryptocaryon irritans in a marine fish farm from Hong Kong

The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as a model to understand the parasite abundance and potential drivers of its presence in marine fish farms. Environmental (rainfall) and physical-chemical (temperature, oxygen, salinity, pH) data collected from a marine fish farm in Hong Kong were analyzed together with the eDNA approach targeting C. irritans abundance based on digital droplet PCR and 16S metagenomics to determine associations and triggers between parasites and specific bacterial groups. Rainfall and temperature demonstrated positive associations with high abundance of C. irritans (eDNA) at the studied marine fish cage farm. However, rainfall was the only parameter tested that demonstrated a significant association with parasite eDNA, indicating that the raining season is a risky period for fish farmers in Hong Kong. Coraliomargarita was the bacterial genus with the most significant relationship with low abundance of C. irritans in water. Understanding the environmental triggers of ciliate parasites propagation and associated bacterial microbiome could elucidate new insights into environmental control, microbial management, and promote the reduction of chemical use in marine fish farms

Psychometric validation of the reintegration to normal living index in people living with spinal cord injuries

The evaluation of rehabilitation outcomes requires measurement instruments that are valid and reliable, and have been psychometrically tested in the context of a particular population. The purpose of this study was to psychometrically test the validity and reliability of the Reintegration to Normal Living Index (RNLI) as a measure of community reintegration in a population of community-dwelling people living with spinal cord injury (PLWSCI) in South Africa. The study was a cross-sectional, involving community dwelling people living with SCI (PLWSCI), who had been discharged from inpatient rehabilitation at for at least two years. RNLI data collected from 160 PLWSCI were subjected to factor analysis and tested for reliability using chronbach’s alpha. Cronbach’s alpha for the RNLI instrument was 0.97 (ICC 95% CI: 0.97 – 0.98), indicating an excellent reliability coefficient. A single -factor structure emerged from principal components analysis, indicating that there is only one factor structure for the RNLI in this population of PLWSCI. The content, construct, convergent and discriminate validity of the instrument were established. The results of this study support the reliability and factorial validity of the RNLI as a measure of community reintegration for PLWSCI. The RNLI is therefore a valuable outcome measure and should be extended to other SCI rehabilitation studies in South Africa.This paper reports on part of a PhD study conducted by DJ Mothabeng at the University of Pretoria, supervised by Dr CA Eksteen and Professor M Westaway.The study was supported by grants from the School of Health Care Sciences at the University of Pretoria, and the Research foundation of the South African Society of Physiotherapy.http://www.sajp.co.za/index.php/sajpam201

The November 2017 Mw 5.5 Pohang earthquake: a possible case of induced seismicity in South Korea

The Mw 5.5 earthquake that struck South Korea in November 2017 was one of the largest and most damaging events in this country over the last century. Its proximity to an Enhanced Geothermal Systems site, where high pressure hydraulic injection had been performed during the previous two years, raises the possibility that this earthquake was anthropogenic. We have combined seismological and geodetic analyses to characterize the mainshock and its largest aftershocks, constrain the geometry of this seismic sequence and shed light on its casual factors. According to our analysis it seems plausible that the occurrence of this earthquake was influenced by these industrial activities. Finally we found that the earthquake transferred static stress to larger nearby faults, potentially increasing the seismic hazard in the area