Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-06-18DOI: 10.1186/jbiol154
Heikki Helanterä
{"title":"Do unicolonial wood ants favor kin?","authors":"Heikki Helanterä","doi":"10.1186/jbiol154","DOIUrl":"https://doi.org/10.1186/jbiol154","url":null,"abstract":"<p><p>Vast supercolonies of interconnected nests formed by unicolonial ant species are the largest cooperative groups of animals known. Research published recently in BMC Evolutionary Biology reveals that a supercolony can be more genetically structured than previously thought, comprising several extended families. Surprisingly, the families coexist peacefully, even though they seem to recognize each other as non-kin.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 6","pages":"56"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28296723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-02-23DOI: 10.1186/jbiol119
Charles F Stevens
{"title":"Darwin and Huxley revisited: the origin of allometry.","authors":"Charles F Stevens","doi":"10.1186/jbiol119","DOIUrl":"https://doi.org/10.1186/jbiol119","url":null,"abstract":"<p><p>The relative sizes of parts of an organism frequently depend on the absolute size of the individual, a relationship that is generally described by power laws. I show here that these power laws are a consequence of the way evolution operates.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 2","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol119","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28048446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-02-06DOI: 10.1186/jbiol116
Joost M Woltering, Denis Duboule
{"title":"Conserved elements within open reading frames of mammalian Hox genes.","authors":"Joost M Woltering, Denis Duboule","doi":"10.1186/jbiol116","DOIUrl":"https://doi.org/10.1186/jbiol116","url":null,"abstract":"<p><p>A recent study in BMC Evolutionary Biology shows that many of the open reading frames in mammalian Hox genes are more conserved than expected on the basis of their protein sequence. The presence of highly conserved DNA elements is thus not confined to the noncoding DNA in neighboring regions but clearly overlaps with coding sequences. These findings support an emerging view that gene regulatory and coding sequences are likely to be more intermingled than once believed.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 2","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27992083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-03-09DOI: 10.1186/jbiol125
Virginia Walbot
{"title":"Are we training pit bulls to review our manuscripts?","authors":"Virginia Walbot","doi":"10.1186/jbiol125","DOIUrl":"https://doi.org/10.1186/jbiol125","url":null,"abstract":"<p><p>Good early training of graduate students and postdocs is needed to prevent them turning into future generations of manuscript-savaging reviewers. How can we intercalate typical papers into our training?</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 3","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28125882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-05-22DOI: 10.1186/jbiol144
Frederick P Roth, Howard D Lipshitz, Brenda J Andrews
{"title":"Q&A: epistasis.","authors":"Frederick P Roth, Howard D Lipshitz, Brenda J Andrews","doi":"10.1186/jbiol144","DOIUrl":"https://doi.org/10.1186/jbiol144","url":null,"abstract":"","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 4","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28212581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-08-11DOI: 10.1186/jbiol168
Lucy Dalton-Griffin, Paul Kellam
{"title":"Infectious causes of cancer and their detection.","authors":"Lucy Dalton-Griffin, Paul Kellam","doi":"10.1186/jbiol168","DOIUrl":"https://doi.org/10.1186/jbiol168","url":null,"abstract":"<p><p>Molecular techniques for identifying pathogens associated with cancer continue to be developed, including one reported recently in BMC Medical Genomics. Identifying a causal infectious agent helps in understanding the biology of these cancers and can lead ultimately to the development of antimicrobial drugs and vaccines for their treatment and prevention.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 7","pages":"67"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol168","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28412527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-12-24DOI: 10.1186/jbiol209
Miranda Robertson
{"title":"Gene regulation, evolvability and the limits of genomics.","authors":"Miranda Robertson","doi":"10.1186/jbiol209","DOIUrl":"https://doi.org/10.1186/jbiol209","url":null,"abstract":"","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 11","pages":"94"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol209","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28641213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-06-22DOI: 10.1186/jbiol156
Elizabeth S Dennis, W James Peacock
{"title":"Vernalization in cereals.","authors":"Elizabeth S Dennis, W James Peacock","doi":"10.1186/jbiol156","DOIUrl":"https://doi.org/10.1186/jbiol156","url":null,"abstract":"<p><p>How vernalization - exposure to a period of cold - induces flowering in Arabidopsis has been intensively investigated at the genetic and moleular levels. Recent papers, including one in BMC Plant Biology, shed light on changes in gene regulation that occur on vernalization in cereals.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 6","pages":"57"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol156","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28296724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-07-13DOI: 10.1186/jbiol159
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
{"title":"Search for a 'Tree of Life' in the thicket of the phylogenetic forest.","authors":"Pere Puigbò, Yuri I Wolf, Eugene V Koonin","doi":"10.1186/jbiol159","DOIUrl":"https://doi.org/10.1186/jbiol159","url":null,"abstract":"<p><strong>Background: </strong>Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.</p><p><strong>Results: </strong>A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.</p><p><strong>Conclusions: </strong>Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 6","pages":"59"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28374983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of BiologyPub Date : 2009-01-01Epub Date: 2009-05-29DOI: 10.1186/jbiol150
Louis Du Pasquier
{"title":"Fish 'n' TRIMs.","authors":"Louis Du Pasquier","doi":"10.1186/jbiol150","DOIUrl":"https://doi.org/10.1186/jbiol150","url":null,"abstract":"<p><p>A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology. The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 5","pages":"50"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28237207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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