RATT: Rapid Annotation Transfer Tool

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net

Wireless Avionics Packet to Support Fault Tolerance for Flight Applications

In this protocol and packet format, data traffic is monitored by all network interfaces to determine the health of transmitter and subsystems. When failures are detected, the network inter face applies its recover y policies to provide continued service despite the presence of faults. The protocol, packet format, and inter face are independent of the data link technology used. The current demonstration system supports both commercial off-the-shelf wireless connections and wired Ethernet connections. Other technologies such as 1553 or serial data links can be used for the network backbone. The Wireless Avionics packet is divided into three parts: a header, a data payload, and a checksum. The header has the following components: magic number, version, quality of service, time to live, sending transceiver, function code, payload length, source Application Data Interface (ADI) address, destination ADI address, sending node address, target node address, and a sequence number. The magic number is used to identify WAV packets, and allows the packet format to be updated in the future. The quality of service field allows routing decisions to be made based on this value and can be used to route critical management data over a dedicated channel. The time to live value is used to discard misrouted packets while the source transceiver is updated at each hop. This information is used to monitor the health of each transceiver in the network. To identify the packet type, the function code is used. Besides having a regular data packet, the system supports diagnostic packets for fault detection and isolation. The payload length specifies the number of data bytes in the payload, and this supports variable-length packets in the network. The source ADI is the address of the originating interface. This can be used by the destination application to identify the originating source of the packet where the address consists of a subnet, subsystem class within the subnet, a subsystem unit, and the local ADI number. The destination ADI is used to route the packet to its ultimate destination. At each hop, the sending interface uses the destination address to determine the next node for the data. The sending node is the node address of the interface that is broadcasting the packet. This field is used to determine the health of the subsystem that is sending the packet. In the case of a packet that traverses several intermediate nodes, it may be the node address of the intermediate node. The target node is the node address of the next hop for the packet. It may be an intermediate node, or the final destination for the packet. The sequence number is used to identify duplicate packets. Because each interface has multiple transceivers, the same packet will appear at both receivers. The sequence number allows the interface to correlate the reception and forward a single, unique packet for additional processing. The subnet field allows data traffic to be partitioned into segregated local networks to support large networks while keeping each subnet at a manageable size. This also keeps the routing table small enough so routing can be done by a simple table lookup in an FPGA device. The subsystem class identifies members of a set of redundant subsystems, and, in a hot standby configuration, all members of the subsystem class will receive the data packets. Only the active subsystem will generate data traffic. Specific units in a class of redundant units can be identified and, if the hot standby configuration is not used, packets will be directed to a specific subsystem unit

Interface Supports Lightweight Subsystem Routing for Flight Applications

A wireless avionics interface exploits the constrained nature of data networks in flight systems to use a lightweight routing method. This simplified routing means that a processor is not required, and the logic can be implemented as an intellectual property (IP) core in a field-programmable gate array (FPGA). The FPGA can be shared with the flight subsystem application. In addition, the router is aware of redundant subsystems, and can be configured to provide hot standby support as part of the interface. This simplifies implementation of flight applications requiring hot stand - by support. When a valid inbound packet is received from the network, the destination node address is inspected to determine whether the packet is to be processed by this node. Each node has routing tables for the next neighbor node to guide the packet to the destination node. If it is to be processed, the final packet destination is inspected to determine whether the packet is to be forwarded to another node, or routed locally. If the packet is local, it is sent to an Applications Data Interface (ADI), which is attached to a local flight application. Under this scheme, an interface can support many applications in a subsystem supporting a high level of subsystem integration. If the packet is to be forwarded to another node, it is sent to the outbound packet router. The outbound packet router receives packets from an ADI or a packet to be forwarded. It then uses a lookup table to determine the next destination for the packet. Upon detecting a remote subsystem failure, the routing table can be updated to autonomously bypass the failed subsystem

Elimination of Schistosoma mansoni Adult Worms by Rhesus Macaques: Basis for a Therapeutic Vaccine?

Infection with blood-dwelling schistosome worms is a major cause of human disease in many tropical countries. Despite intensive efforts a vaccine has proved elusive, not least because the chronic nature of the infection provides few pointers for vaccine development. The rhesus macaque appears unique among animal models in that adult worms establish but are eventually lost. We investigated whether this was due to pathological or immunological causes by monitoring the fate of a schistosome infection, and were able to rule out escape of worms from the portal system as a result of egg-induced vascular shunts. A substantial worm population established in all animals but there was a wide variation in the numbers recovered at 18 weeks. We observed a strong inverse association between the rapidity and intensity of the IgG response and worm burden. Rather than an acute lethal attack, immune-mediated elimination of worms appeared to be a prolonged process directed against vital components of exposed surfaces, causing worms to starve to death. We suggest that if the mechanisms deployed by the rhesus macaque could be replicated in humans by administration of key recombinant antigens, they would form the basis for a vaccine with both prophylactic and therapeutic properties

Tousled-like Kinases Modulate Reactivation of Gammaherpesviruses from Latency

Kaposi’s sarcoma-associated herpesvirus (KSHV) is linked to human malignancies. The majority of tumor cells harbor latent virus and a small percentage undergo spontaneous lytic replication. Both latency and lytic replication are important for viral pathogenesis and spread but the cellular players involved in the switch between the two viral lifecycle phases are not clearly understood. We conducted a siRNA screen targeting the cellular kinome and identified Tousled-like kinases (TLKs) as cellular kinases that control KSHV reactivation from latency. Upon treatment of latent KSHV-infected cells with siRNAs targeting TLKs, we saw robust viral reactivation. Knockdown of TLKs in latent KSHV-infected cells induced expression of viral lytic proteins and production of infectious virus. TLKs were also found to play a role in regulating reactivation from latency of another related oncogenic gammaherpesvirus, Epstein-Barr virus (EBV). Our results establish the TLKs as cellular repressors of gammaherpesviral reactivation

Acupuncture for dyspnea in advanced cancer: a randomized, placebo-controlled pilot trial [ISRCTN89462491]

BACKGROUND: Dyspnea, or shortness of breath, is a common symptom in patients with advanced cancer. Pharmacologic management is of proven benefit, but it does not help all patients. Preliminary data suggest that acupuncture can relieve dyspnea in a variety of populations, including cancer patients. We conducted a pilot study (ISRCTN89462491) preparatory to a fully powered randomized, placebo-controlled trial to determine whether acupuncture reduces dyspnea in patients with lung or breast cancer. METHODS: The study sample was comprised of forty-seven patients with lung or breast cancer presenting with dyspnea. Patients receiving symptomatic treatments were not excluded as long as no changes in management were planned during the trial. Patients were randomized to receive a single session of true or placebo acupuncture in addition to their existing dyspnea treatments. Semi-permanent acupuncture "studs" were then inserted: patients applied pressure to these studs twice a day to provide ongoing stimulation to acupuncture points. The subjective sensation of dyspnea was assessed with a 0 – 10 numerical rating scale immediately before and after acupuncture treatment and daily for a week thereafter. RESULTS: All but two of 47 randomized patients provided follow-up data. Dyspnea scores were slightly higher for patients receiving true versus placebo acupuncture, for both the period immediately following acupuncture treatment and for the daily one week follow-up (differences between means of 0.34, 95% C.I. -0.33, 1.02 and 0.56, 95% C.I. -0.39, 1.51). The 95% confidence interval excludes the prespecified minimum clinically significant difference of a 20% greater improvement in dyspnea for patients receiving acupuncture. CONCLUSION: The acupuncture technique used in this trial is unlikely to have effects on dyspnea importantly larger than placebo for patients with advanced cancer

'To live and die [for] Dixie': Irish civilians and the Confederate States of America

Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism

Altered Patterns of Gene Expression Underlying the Enhanced Immunogenicity of Radiation-Attenuated Schistosomes

Schistosoma mansoni is a blood-dwelling parasitic worm that causes schistosomiasis in humans throughout Africa and parts of South America. A vaccine would enhance attempts to control and eradicate the disease that currently relies on treatment with a single drug. Although a manufactured vaccine has yet to generate high levels of protection, this can be achieved with infective parasite larvae that have been disabled by exposure to radiation. How these weakened parasites are able to induce protective immunity when normal parasites do not, is the question addressed by our experiments. We have used a technique of gene expression profiling to compare the patterns in normal and disabled parasites, over the period when they would trigger an immune response in the host. We found that only a handful of genes were differentially expressed, all of them diminished in the disabled parasite. However, a more sensitive technique to examine groups of genes revealed that those involved in nervous system and muscle function were depressed in the disabled parasites. We suggest that reduced mobility of these larvae permits them longer contact with the immune system, thus enabling a strong protective immune response to develop

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host

The schistosome cercaria develops from undifferentiated germ balls within the daughter sporocyst located in the hepatopancreas of its snail intermediate host. This is where the proteins it uses to infect humans are synthesised. After a brief free life in fresh water, if the cercaria locates a host, it infects by direct penetration through the skin. It then transforms into the schistosomulum stage, adapted for life in human tissues. We have designed a large scale array comprising probes representing all known schistosome genes and used it in hybridisation experiments to establish which genes are turned on or off in the parasite during these stages in its life cycle. Genes encoding proteins involved in cell division were prominent in the germ ball along with those for proteases and potential immunomodulators, deployed during skin penetration. The non-feeding cercaria was the least active at synthesising proteins. Conversion to the schistosomulum was accompanied by transcription of genes involved in body remodeling, including production of a new outer surface, and gut activation long before ingestion of red blood cells begins. Our data help us to understand better the proteins deployed to achieve infection, and subsequent adaptations necessary for establishment of the parasite in the human host