Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach

This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models with tree-structured shrinkage. The proposed approach enables (1) borrowing of information across leaves, (2) estimating data-driven leaf groups with distinct vectors of class probabilities, and (3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.     

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.     

Genome-wide identification,classification, and expression profiling of serine esterases and other esterase-related proteins in the tobacco hornworm,Manduca sexta

Serine esterases (SEs) are hydrolases that catalyze the conversion of carboxylic esters into acids and alcohols. Lipases and carboxylesterases constitute two major groups of SEs. Although over a hundred of insect genomes are known, systematic identification and classification of SEs are rarely performed, likely due to large size and complex composition of the gene family in each species. Considering their key roles in lipid metabolism and other physiological processes, we have categorized 144 M. sexta SEs and SE homologs (SEHs), 114 of which contain a motif of GXSXG. Multiple sequence alignment and phylogenetic tree analysis have revealed 39 neutral lipases (NLs), 3 neutral lipase homologs (NLHs), 11 acidic lipases (ALs), 3 acidic lipase homologs (ALHs), a lipase-3, a triglyceride lipase, a monoglyceride lipase, a hormone-sensitive lipase, and a GDSL lipase. Eighty-three carboxylesterase genes encode 29 α-esterases (AEs), 12 AEHs (e.g., SEH4-1–3), 20 feruloyl esterases (FEs), 2 FEHs, 2 β-esterases (BEs), 2 integument esterases (IEs), 1 IEH, 4 juvenile hormone esterases, 2 acetylcholinesterases, gliotactin, 6 neuroligins, neurotactin, and an uncharacteristic esterase homolog. In addition to these GXSXG proteins, we have identified 26 phospholipases and 13 thioesterases. Expression profiling of these genes in specific tissues and stages has provided insights into their functions including digestion, detoxification, hormone processing, neurotransmission, reproduction, and developmental regulation. In summary, we have established a framework of information on SEs and related proteins in M. sexta to stimulate their research in the model species and comparative investigations in agricultural pests or disease vectors.     

DEVELOPMENTAL MUTANTS OF VOLVOX: DOES MUTATION RECREATE THE PATTERNS OF PHYLOGENETIC DIVERSITY?

The nature of the variation which is created by mutation can show how the direction of evolution is constrained by internal biases arising from development and pre-existing design. We have attempted to quantify these biases by measuring eight life history characters in developmental mutants of Volvox carteri. Most of the mutants in our sample were inferior to the wild type, but deviated by less than tenfold from the wild-type mean. Characters differed in mutability, suggesting different levels of canalisation. Most correlations between life history characters among strains were positive, but there was a significant negative correlation between the size and the number of reproductive cells, suggesting an upper limit to the total quantity of germ produced by individuals. The most extreme phenotypes in our sample were very vigorous, showing that not all mutations of large effect are unconditionally deleterious. We investigated the effect of developmental constraints on the course of evolution by comparing the variance and covariance patterns among mutant strains with those among species in the family Volvocaceae. A close correspondence between patterns at these two levels would suggest that pre-existing design has a strong influence on evolution, while little or no correspondence shows the action of selection. The variance generated by mutation was equal to that generated by speciation in the family Volvocaceae, the genus Volvox, or the section Merillosphaera, depending on the character considered. We found that mutation changes the volume of somatic tissue independently of the quantity of germ tissue, so that the interspecific correlation between soma and germ can be attributed to selection. The negative correlation between size and number of germ cells among mutants of V. carteri is also seen among the larger members of the family (Volvox spp.), but not among the smaller members, suggesting a powerful design constraint that may be responsible for the absence of larger forms in the entire group.     

DNA水平上的植物系统学研究方法

本文简要总结了近年来在ＤＮＡ水平上的植物系统学研究方法,着重介绍了限制性长度多态性分析,ＰＣＲ技术在植物系统学上的应用等这一领域最新的进展,并对分子数据的分析方法及系统树的构建进行了详细讨论。     

Sarsicopia polaris gen. et sp.n., the first platycopioida (Copepoda: Crustacea) from the Arctic Ocean,and its phylogenetic significance

A new genus of Platycopioida is described from a boxcore sample taken at a depth of 534 m in the ArcticBarents Sea. This is the deepest record ofPlatycopioida so far. Sarsicopia gen. n. is thesistergroup of a taxon comprising Platycopia and Nanocopia; the sistergroup ofthese is Antrisocopia. Sarsicopia gen. n.is the only platycopioid to retain 2 inner setae onthe second endopod segment P2–P4, and 8 setae in thethird endopod segment of P2. The male antennnule isremarkable in having a geniculation located betweenancestral segments XX and XXI. It is suggested thatthis flexure zone was already present in thegroundpattern of Copepoda. Platycopia and Nanocopia have secondarily lost thisgeniculation.     

A phylogenetic study of the free-living amoeba

Immunological distances were determined for four strains of the free-living amoeba classified as Amoeba proteus, two strains classified as Polychaos dubia and a single strain classified as Chaos carolinensis. The data show that the _ShP strain does not belong to the proteus group; that A. proteus is more closely related to C. carolinensis and is derived from Chaos as is the _ShP strain; that P. dubia and C. carolinensis are the more distantly related species and appear to be the first of the above to have diverged from a common ancestor; and that the amoebae have a long evolutionary history. The accuracy of the phylogenetic tree and the distance Wagner network was discussed. Since the amoebae may be polyphyletic in origin, the latter was assumed to be a more accurate representation of the immunological distance data.     

Genetic control of hexokinase variation in insects

Hexokinase variation in insects appears to be under the control of a single locus in some species and under multiple-locus control in others. It is often difficult to distinguish the number of loci controlling hexokinase expression. Analysis of hexokinase electrophoretic patterns in six species of mosquitoes and five species of crickets, as well as a review of hexokinase variation in other insect species, is used to emphasize the importance of interspecific comparisons when making genetic inferences. Evidence is provided which adds support for multiple hexokinase loci in dipterans. Hexokinase control by multiple loci may be difficult to determine in some species because of tight linkage, disequilibrium, and/or posttranslational modification.This work was supported by NIH Grant AI 11132-09, NSF Grant DEB-7811188, and Yale Sesil Anonymous Funds.     

In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs

A method to investigate the structure of RNA molecules within intact plant tissues has been developed. The RNA structures are analyzed using dimethyl sulfate (DMS), which modifies substituents of adenine and cytosine residues within single-stranded regions of RNA molecules. Reactive sites are identified by primer extension analysis. Using this procedure, an analysis of the secondary structure of the cytoplasmic 18S ribosomal RNA in soybean seedling leaves has been completed. DMS modification data are in good agreement with the phylogenetic structure predicted for soybean 18S rRNA. However, there are a few notable exceptions where residues thought to be involved in double-stranded regions in all 18S rRNAs are strongly modified in soybean leaf samples. These data taken together with the phylogenetic structure suggest that alternate structures may exist in vivo.The further applicability of this technique is demonstrated by comparing the modification pattern obtained in vivo to that obtained in vitro for a particular mRNA molecule encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. The results obtained are compared to a predicted minimum energy secondary structure. The data indicate that the conformation of RNA molecules within the cell may not be reflected in a structural analysis of purified mRNA molecules.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.