Evolutionary rates for tuf genes in endosymbionts of aphids

The gene encoding elongation factor Tu (tuf) in aphid endosymbionts (genus Buchnera) evolves at rates of 1.3 x 10(-10) to 2.5 x 10(-10) nonsynonymous substitutions and 3.9 x 10(-9) to 8.0 x 10(-9) synonymous substitutions per position per year. These rates, which are at present among the most reliable substitution rates for protein-coding genes of bacteria, have been obtained by calibrating the nodes in the phylogenetic tree produced from the Buchnera EF-Tu sequences using divergence times for the corresponding ancestral aphid hosts. We also present data suggesting that the rates of nonsynonymous substitutions are significantly higher in the endosymbiont lineages than in the closely related free-living bacteria Escherichia coli and Salmonella typhimurium. Synonymous substitution rates for Buchnera approximate estimated mutation rates for E. coli and S. typhimurium, as expected if synonymous changes act as neutral mutations in Buchnera. We relate the observed differences in substitution frequencies to the absence of selective codon preferences in Buchnera and to the influence of Muller's ratchet on small asexual populations.      

Host Resistance in Relation to Survival in Breast Cancer

The degree of lymphocytic infiltration in and around breast tumours together with sinus histiocytosis and follicular hyperplasia in regional lymph nodes has been studied in 310 cases of breast cancer treated with standard radical mastectomy. The presence of these features was regarded as evidence of host resistance against the tumour and made possible the division of patients into three classes—no or poor reaction, good reaction, and strong reaction. The grading was shown to have a close correlation with prognosis. The relationship between host defensive factor grading and malignancy, nodal metastases, and survival was also examined. The results support the hypothesis that prognosis in breast cancer is closely related to a histological picture of cell-mediated immunity against the tumour.     

Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response

PERK and IRE1 are type-I transmembrane protein kinases that reside in the endoplasmic reticulum (ER) and transmit stress signals in response to perturbation of protein folding. Here we show that the lumenal domains of these two proteins are functionally interchangeable in mediating an ER stress response and that, in unstressed cells, both lumenal domains form a stable complex with the ER chaperone BiP. Perturbation of protein folding promotes reversible dissociation of BiP from the lumenal domains of PERK and IRE1. Loss of BiP correlates with the formation of high-molecular-mass complexes of activated PERK or IRE1, and overexpression of BiP attenuates their activation. These findings are consistent with a model in which BiP represses signalling through PERK and IRE1 and protein misfolding relieves this repression by effecting the release of BiP from the PERK and IRE1 lumenal domains.     

Coronavirus and paramyxovirus in bats from Northwest Italy

Background

Bat-borne virus surveillance is necessary for determining inter-species transmission risks and is important due to the wide-range of bat species which may harbour potential pathogens. This study aimed to monitor coronaviruses (CoVs) and paramyxoviruses (PMVs) in bats roosting in northwest Italian regions. Our investigation was focused on CoVs and PMVs due to their proven ability to switch host and their zoonotic potential. Here we provide the phylogenetic characterization of the highly conserved polymerase gene fragments.

Results

Family-wide PCR screenings were used to test 302 bats belonging to 19 different bat species. Thirty-eight animals from 12 locations were confirmed as PCR positive, with an overall detection rate of 12.6% [95% CI: 9.3–16.8]. CoV RNA was found in 36 bats belonging to eight species, while PMV RNA in three Pipistrellus spp. Phylogenetic characterization have been obtained for 15 alpha- CoVs, 5 beta-CoVs and three PMVs; moreover one P. pipistrellus resulted co-infected with both CoV and PMV. A divergent alpha-CoV clade from Myotis nattereri SpA is also described. The compact cluster of beta-CoVs from R. ferrumequinum roosts expands the current viral sequence database, specifically for this species in Europe. To our knowledge this is the first report of CoVs in Plecotus auritus and M. oxygnathus, and of PMVs in P. kuhlii.

Conclusions

This study identified alpha and beta-CoVs in new bat species and in previously unsurveyed Italian regions. To our knowledge this represents the first and unique report of PMVs in Italy. The 23 new bat genetic sequences presented will expand the current molecular bat-borne virus databases. Considering the amount of novel bat-borne PMVs associated with the emergence of zoonotic infections in animals and humans in the last years, the definition of viral diversity within European bat species is needed. Performing surveillance studies within a specific geographic area can provide awareness of viral burden where bats roost in close proximity to spillover hosts, and form the basis for the appropriate control measures against potential threats for public health and optimal management of bats and their habitats.

     

Cellular responses to halofuginone reveal a vulnerability of the GCN2 branch of the integrated stress response

Halofuginone (HF) is a phase 2 clinical compound that inhibits the glutamyl‐prolyl‐tRNA synthetase (EPRS) thereby inducing the integrated stress response (ISR). Here, we report that halofuginone indeed triggers the predicted canonical ISR adaptations, consisting of attenuation of protein synthesis and gene expression reprogramming. However, the former is surprisingly atypical and occurs to a similar magnitude in wild‐type cells, cells lacking GCN2 and those incapable of phosphorylating eIF2α. Proline supplementation rescues the observed HF‐induced changes indicating that they result from inhibition of EPRS. The failure of the GCN2‐to‐eIF2α pathway to elicit a measurable protective attenuation of translation initiation allows translation elongation defects to prevail upon HF treatment. Exploiting this vulnerability of the ISR, we show that cancer cells with increased proline dependency are more sensitive to halofuginone. This work reveals that the consequences of EPRS inhibition are more complex than anticipated and provides novel insights into ISR signaling, as well as a molecular framework to guide the targeted development of halofuginone as a therapeutic.     

Characterization of 13 newly isolated strains of anaerobic, cellulolytic, thermophilic bacteria

Characteristics of 13 newly isolated thermophilic, anaerobic, and cellulolytic strains were compared with previously described strains of Clostridium thermocellum: ATCC 27405 and JW20 (ATCC 31549). Colony morphology, antibiotic sensitivity, fermentation end-products, and cellulose degradation were documented. All 13 strains were sensitive to erythromycin (5 μg/ml) and chloramphenicol (25 μg/ml), and all strains but one were sensitive to kanamycin (20 μg/ml). Polymerase chain reaction (PCR) amplification using primers based on gene sequences from C. thermocellum ATCC 27405 was successful for all 13 strains in the case of the hydrogenase gene and 11 strains in the case of phosphotransacetylase/acetate kinase genes. Ten strains amplified a product of the expected size with primers developed to be specific for C. thermocellum 16SrRNA primers. Two of the 13 strains did not amplify any product with the PCR primers designed for the phosphotransacetylase/acetate kinase and 16SrRNA primers. A MboI-like GATC- recognizing restriction activity was present in all of the five strains examined. The results of this study have several positive implications with respect to future development of a transformation system for cellulolytic thermophiles. Journal of Industrial Microbiology & Biotechnology (2001) 27, 275–280. Received 12 September 2000/ Accepted in revised form 20 November 2000     

Modeling the spread of vector-borne diseases on bipartite networks

Background

Vector-borne diseases for which transmission occurs exclusively between vectors and hosts can be modeled as spreading on a bipartite network.

Methodology/Principal Findings

In such models the spreading of the disease strongly depends on the degree distribution of the two classes of nodes. It is sufficient for one of the classes to have a scale-free degree distribution with a slow enough decay for the network to have asymptotically vanishing epidemic threshold. Data on the distribution of Ixodes ricinus ticks on mice and lizards from two independent studies are well described by a scale-free distribution compatible with an asymptotically vanishing epidemic threshold. The commonly used negative binomial, instead, cannot describe the right tail of the empirical distribution.

Conclusions/Significance

The extreme aggregation of vectors on hosts, described by the power-law decay of the degree distribution, makes the epidemic threshold decrease with the size of the network and vanish asymptotically.     

Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008

Highly pathogenic A/H5N1 avian influenza (HPAI H5N1) viruses have seriously affected the Nigerian poultry industry since early 2006. Previous studies have identified multiple introductions of the virus into Nigeria and several reassortment events between cocirculating lineages. To determine the spatial, evolutionary, and population dynamics of the multiple H5N1 lineages cocirculating in Nigeria, we conducted a phylogenetic analysis of whole-genome sequences from 106 HPAI H5N1 viruses isolated between 2006 and 2008 and representing all 25 Nigerian states and the Federal Capital Territory (FCT) reporting outbreaks. We identified a major new subclade in Nigeria that is phylogenetically distinguishable from all previously identified sublineages, as well as two novel reassortment events. A detailed analysis of viral phylogeography identified two major source populations for the HPAI H5N1 virus in Nigeria, one in a major commercial poultry area (southwest region) and one in northern Nigeria, where contact between wild birds and backyard poultry is frequent. These findings suggested that migratory birds from Eastern Europe or Russia may serve an important role in the introduction of HPAI H5N1 viruses into Nigeria, although virus spread through the movement of poultry and poultry products cannot be excluded. Our study provides new insight into the genesis and evolution of H5N1 influenza viruses in Nigeria and has important implications for targeting surveillance efforts to rapidly identify the spread of the virus into and within Nigeria.Since its emergence in 1996 in Guangdong, China, highly pathogenic avian influenza virus of the H5N1 subtype (HPAI H5N1 virus) has disseminated widely across Asia, Europe, and Africa, infecting a range of domestic and wild avian species and sporadically spilling over into humans and other mammals (4, 35). Over time, the HPAI H5N1 virus has diversified into multiple phylogenetically distinct lineages, classified as clades 0 to 9 according to the unified nomenclature system (33). The H5N1 lineage currently circulating in central Asia, the Middle East, Europe, and Africa is referred to as clade 2.2 (33) and has also been described as “EMA” or Qinghai-like in previous publications (4, 17, 27). This clade originated in April 2005 during a large outbreak of a phylogenetically distinct H5N1 virus among wild bird populations at Qinghai Lake in western China (4, 17) and rapidly spread west through central Asia and Europe, eventually reaching Africa in 2006 (27). Clade 2.2 has further diversified, forming the genetic third-order clade 2.2.1 (32) and three genetically distinct sublineages (I, II, and III) (2, 19, 28), all of which are found in Africa.Since 2006 HPAI H5N1 viruses belonging to clade 2.2 have disseminated across multiple countries in western, eastern, and northern Africa: Egypt, Niger, Cameroon, Sudan, Burkina Faso, Djibouti, Ivory Coast, Ghana, Togo, Benin, and Nigeria (2). With a large poultry industry, estimated at 140 million birds (11), Nigeria has experienced several major outbreaks of HPAI H5N1 virus, posing a serious threat to food security and public health in Africa. The first case of HPAI H5N1 virus in Nigeria (sublineage I) occurred in January 2006 in the state of Kaduna, and the virus subsequently was detected in Ghana, Burkina Faso, Ivory Coast, and Sudan (2). In February 2006 sublineage II was reported in Nigeria, and it disseminated widely across the country during 2006 and 2007, also appearing in Togo (2). Clade 2.2.1, which has been prevalent in Egypt, Israel, and the Gaza Strip from 2006 to 2008, was also detected in Nigeria in 2006 (10).By the end of 2007, outbreaks of HPAI H5N1 virus in Nigeria appeared to have been successfully controlled by measures such as “stamping out with compensation,” restrictions on movement of poultry, and enhanced surveillance (13). However, in July 2008 new cases of HPAI H5N1 from a sublineage never previously detected in Africa (sublineage III) were registered in the Nigerian states of Kano and Katsina and in live bird markets in Gombe and Kebbi states (13, 21). Hence, Nigeria is the only African country where viruses belonging to clade 2.2.1 and to three different sublineages (I, II, and III) of clade 2.2 have all been detected. At least three different reassortment events between sublineages have been documented in Nigeria. Salzberg et al. identified the first reassortant strain (which we refer to as “R1”), in which four genome segments (hemagglutinin [HA], NP, NS, and PB1) belong to sublineage I and the other four segments (NA, MP, PA, and PB2) are derived from sublineage II (27). Subsequently, phylogenetic analysis showed that a 2007 reassortant strain (which we refer to as “R3”) contained the HA and NS segments from sublineage I and the other six segments from sublineage II (19, 22). Another reassortant virus (which we refer to as “R5”) contained only the NS gene segment from sublineage I, while the other seven segments were derived from sublineage II (22).Although the genetic diversity of the Nigerian HPAI H5N1 virus population has been well characterized, including multiple introductions of the virus into Nigeria and several reassortment events, little is known about the evolutionary and population growth dynamics of the virus within Nigeria. Particularly understudied are the spatial movements of individual sublineages among Nigeria''s vast poultry population. To explore the spatial, evolutionary, and population dynamics of the multiple H5N1 lineages cocirculating in Nigeria, we conducted a phylogenetic analysis of whole-genome sequences from 106 HPAI H5N1 viruses isolated between 2006 and 2008 and representing all 25 Nigerian states and the Federal Capital Territory (FCT) reporting outbreaks. Using the exact date and location of collection for each viral isolate, we inferred from their phylogenetic relationships the directionality of viral gene flow among Nigerian states and identified critical regions that are likely to serve as key sources for the H5N1 virus in Nigeria.