RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.

Over 50% of genes in Plasmodium falciparum, the deadliest human malaria parasite, contain predicted introns, yet experimental characterization of splicing in this organism remains incomplete. We present here a transcriptome-wide characterization of intraerythrocytic splicing events, as captured by RNA-Seq data from four timepoints of a single highly synchronous culture. Gene model-independent analysis of these data in conjunction with publically available RNA-Seq data with HMMSplicer, an in-house developed splice site detection algorithm, revealed a total of 977 new 5' GU-AG 3' and 5 new 5' GC-AG 3' junctions absent from gene models and ESTs (11% increase to the current annotation). In addition, 310 alternative splicing events were detected in 254 (4.5%) genes, most of which truncate open reading frames. Splicing events antisense to gene models were also detected, revealing complex transcriptional arrangements within the parasite's transcriptome. Interestingly, antisense introns overlap sense introns more than would be expected by chance, perhaps indicating a functional relationship between overlapping transcripts or an inherent organizational property of the transcriptome. Independent experimental validation confirmed over 30 new antisense and alternative junctions. Thus, this largest assemblage of new and alternative splicing events to date in Plasmodium falciparum provides a more precise, dynamic view of the parasite's transcriptome

The minimal structure containing the band 3 anion transport site. A 35Cl NMR study

35Cl NMR, which enables observation of chloride binding to the anion transport site on band 3, is used in the present study to determine the minimal structure containing the intact transport site. Removal of cytoskeletal and other nonintegral membrane proteins, or removal of the 40-kDa cytoskeletal domain of band 3, each leave the transport site intact. Similarly, cleavage of the 52-kDa transport domain into 17- and 35-kDa fragments by chymotrypsin leaves the transport site intact. Extensive proteolysis by papain reduces the integral red cell membrane proteins to their transmembrane segments. Papain treatment removes approximately 60% of the extramembrane portion of the transport domain and produces small fragments primarily in the range 3-7 kDa, with 5 kDa being most predominant. Papain treatment damages, but does not destroy, chloride binding to the transport site; thus, the minimal structure containing the transport site is composed solely of transmembrane segments. In short, the results are completely consistent with a picture in which the transport site is buried in the membrane where it is protected from proteolysis; the transmembrane segments that surround the transport site are held together by strong attractive forces within the bilayer; and the transport site is accessed by solution chloride via an anion channel leading from the transport site to the solution

What's Been Happening to Charitable Giving Recently? A Look at the Data

Examines the impact of the recession on giving by individuals, foundations, bequests, and corporations; the effects of tax policy changes on individual giving and bequests; and the potential effects of capping the charitable deduction at 28 percent

Terms in elliptic divisibility sequences divisible by their indices

Let D = (D_n)_{n\ge1} be an elliptic divisibility sequence. We study the set S(D) of indices n satisfying n | D_n. In particular, given an index n in S(D), we explain how to construct elements nd in S(D), where d is either a prime divisor of D_n, or d is the product of the primes in an aliquot cycle for D. We also give bounds for the exceptional indices that are not constructed in this way

Victim-Offender Mediation: What Social & Political Factors Will Affect Its Development?

Published in cooperation with the American Bar Association Section of Dispute Resolutio

"Pricing the major hub airports"

Implementing congestion pricing at twenty-seven major US airports would reduce delays by thirteen passenger-years and one thousand aircraft-hours every day, saving three to five million dollars. Chicago and Atlanta would save about one thousand dollars per aircraft. Airport revenues would increase about eleven million dollars daily. A bottleneck model with stochastic queues estimates substantial welfare gains whether or not airlines internalize self-imposed delays. Erroneously imposing fees from the non-internalizing specification on internalizing airlines, however, would be a costly mistake. The model calculates equilibrium traffic rates, queuing delays, layover times, connection times, and congestion fee schedules by minute of the day.airport congestion pricing, stochastic queuing, bottleneck model.

Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts

DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging π-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain