A comparison of phylogenetic network methods using computer simulation

Background

We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination.

Principal Findings

In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths.

Conclusions

Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.     

Critical interaction of actuator domain residues arginine 174, isoleucine 188, and lysine 205 with modulatory nucleotide in sarcoplasmic reticulum Ca2+-ATPase

ATP plays dual roles in the reaction cycle of the sarcoplasmic reticulum Ca2+-ATPase by acting as the phosphorylating substrate as well as in nonphosphorylating (modulatory) modes accelerating conformational transitions of the enzyme cycle. Here we have examined the involvement of actuator domain residues Arg174, Ile188, Lys204, and Lys205 by mutagenesis. Alanine mutations to these residues had little effect on the interaction of the Ca2E1 state with nucleotide or on the HnE 2 to Ca2E1 transition of the dephosphoenzyme. The phosphoenzyme processing steps, Ca2E1P to E2P and E2P dephosphorylation, and their stimulation by MgATP/ATP were markedly affected by mutations to Arg174, Ile188, and Lys205. Replacement of Ile188 with alanine abolished nucleotide modulation of dephosphorylation but not the modulation of the Ca2E1P to E2P transition. Mutation to Arg174 interfered with nucleotide modulation of either of the phosphoenzyme processing steps, indicating a significant overlap between the modulatory nucleotide-binding sites involved. Mutation to Lys205 enhanced the rates of the phosphoenzyme processing steps in the absence of nucleotide and disrupted the nucleotide modulation of the Ca2E1P to E2P transition. Remarkably, the mutants with alterations to Lys205 showed an anomalous inhibition by ATP of the dephosphorylation, and in the alanine mutant the affinity for the inhibition by ATP was indistinguishable from that for stimulation by ATP of the wild type. Hence, the actuator domain is an important player in the function of ATP as modulator of phosphoenzyme processing, with Arg174, Ile188, and Lys205 all being critically involved, although in different ways. The data support a variable site model for the modulatory effects with the nucleotide binding somewhat differently in each of the conformational states occurring during the transport cycle.     

Plant cell factories as a source for anti-cancer lignans

The review places podophyllotoxin, a powerful anti-cancer material used in clinical treatment of small cell cancers, in focus. The economical synthesis of podophyllotoxin is not feasible and demand for this material outstrips supply. At present, Podophyllum hexandrum (Indian May apple) is the commercial source but it grows in an inhospitable region (the Himalayas) where it is collected from wild stands. Furthermore, the plant is now an endangered species. Alternative sources of podophyllotoxin are considered, e.g., the supply of podophyllotoxin and related lignans by establishing plant cell cultures that can be grown in fermentation vessels. Increase of product yields, by variation of medium and culture conditions or by varying the channelling of precursors into side-branches of the biosynthetic pathway by molecular approaches, are discussed.     

TRANSECTION OF THE PANCREAS BY BLUNT TRAUMA

If a diagnosis of traumatic pancreatitis is made and the patient does not improve clinically during the first 24 hours, transection of the pancreas should be suspected. If this is found to be the case at operation, the distal pancreas should be resected and the proximal end of the pancreas closed carefully with interrupted mattress suture of non-absorbable suture material. Particularly, the pancreatic duct should be ligated to prevent the formation of an external fistula. Any attempt at reapproximation of the transected pancreas will invariably result in an external pancreatic fistula if the patient survives the immediate postoperative period.     

Pseudourea, 2,2′-(9,10-Anthrylenedimethylene) bis-(2-thio-, dihydrochloride) Dihydrate: Microbiological Assay and Tissue Distribution Studies in Mice

A microbiological assay for pseudourea, 2,2′-(9,10-anthrylenedimethylene)bis-(2-thio-, dihydrochloride) dihydrate (NSC 56054), a new anticancer agent, has been developed and tissue distribution studies in mice have been performed.     

Physiological and behavioural responses in the hen (Gallus domesticus) to nociceptive stimulation

1. Physiological and behavioural parameters were examined in the hen in response to a noxious and non-noxious stimulus. 2. Two distinct patterns emerged depending on the type of stimulus (noxious----crouching, non-noxious----wingflapping). 3. The responses seen in the hen to the two different types of stimuli appear to be similar to those occurring in mammals.     

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

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The use of barrier-connected pitfall trapping for sampling predatory beetles and spiders

The efficiency of barrier-connected pitfall trapping was compared to conventional single traps or arrays. For ground-active beetles, the use of a pitfall system incorporating a wetting agent with five traps arranged in a cross formation connected by plastic barriers was more efficient than a single dry trap by at least an order of magnitude and at least twice as efficient as five traps without connecting barriers. It is argued that the efficiency of pitfall trapping may be improved markedly by using barrier-connected traps, particularly for some carabid and staphylinid beetles and lycosid spiders. Capture of linyphiids was not improved by the use of barriers and was dependent only on the use of wetting agent and number of traps used.