In search of noise-induced bimodality

Many biological studies are carried out on large populations of cells, often in order to obtain enough material to make measurements. However, we now know that noise is endemic in biological systems and this results in cell-to-cell variability in what appears to be a population of identical cells. Although often neglected, this noise can have a dramatic effect on system responses to environmental cues with significant and often counter-intuitive biological outcomes. A recent study in BMC Systems Biology provides an example of this, documenting a bimodal distribution of activated extracellular signal-regulated kinase in a population of cells exposed to epidermal growth factor and demonstrating that the observed bimodality of the response is induced purely by noise.See research article: http://www.biomedcentral.com/1752-0509/6/109     

Appetite for destruction: the inhibition of glycolysis as a therapy for tuberous sclerosis complex-related tumors

Rule-based modeling has become a powerful approach for modeling intracellular networks, which are characterized by rich molecular diversity. Truly comprehensive models of cell behavior, however, must address spatial complexity at both the intracellular level and at the level of interacting populations of cells, and will require richer modeling languages and tools. A recent paper in BMC Systems Biology represents a signifcant step toward the development of a unified modeling language and software platform for the development of multi-level, multiscale biological models. See research article: http://www.biomedcentral.com/1752-0509/5/166     

The Year of the Wisent

Delving into European prehistory, two recent studies analyze ancient DNA from bison species depicted by our ancestors on the walls of their caves. The DNA tells a story of migrations driven by climate change but leaves some mystery clouding the genetic descent and climate preference of the still-extant wisent, otherwise known as the European bison.See research articles: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0317-7 http://www.nature.com/articles/ncomms13158     

Opening a can of centipedes: new insights into mechanisms of body segmentation

The search for a common developmental genetic mechanism of body segmentation appears to become more difficult, and more interesting, as new segmented organisms are added to the roster. Recent work in this journal by Brena and Akam on segmentation of the geophilomorph centipede Strigamia maritima, an arthropod distantly related to the standard insect models, contains developmental and evolutionary surprises that highlight the importance of a wider sampling of phyla.See research article: http://www.biomedcentral.com/1741-7007/11/112     

Proteasome inhibition,the pursuit of new cancer therapeutics,and the adaptor molecule p130Cas

Current interest in proteasome inhibitors for cancer therapy has stimulated considerable research efforts to identify the molecular pathway to their cytotoxicity with a view to identifying the mechanisms of sensitivity and resistance as well as informing the development of new drugs. Zhao and Vuori describe this month in BMC Biology experiments indicating a novel role of the adaptor protein p130Cas in sensitivity to apoptosis induced not only by proteasome inhibitors but also by the unrelated drug doxorubicin.See research article: http://www.biomedcentral.com/1741-7007/9/73     

Frugal fat or munificent muscle: genomic imprinting and metabolism

Variation in body composition is a popular obsession. The culturally ‘ideal’ body type is light on fat and heavy on muscle but the human population is collectively laying on fat. A new study finds antagonistic effects of two imprinted genes, Grb10 and Dlk1, on body composition in mice. These findings pose the question whether there is an evolutionary conflict between genes of maternal and paternal origin over the optimal proportions of body fat and lean muscle mass.See research article: http://www.biomedcentral.com/1741-7007/12/771     

Is sex necessary?

Fungal sexual reproductive modes have markedly high diversity and plasticity, and asexual species have been hypothesized to arise frequently from sexual fungal species. A recent study on the red yeasts provides further support for the notion that sexual ancestors may give rise to shorter-lived asexual species. However, presumed asexual species may also be cryptically sexual, as revealed by other recent studies.See research article: http://www.biomedcentral.com/1471-2148/11/249     

The small protein floodgates are opening; now the functional analysis begins

Aside from a few serendipitous discoveries, small proteins of less than 50 amino acids in bacteria and 100 amino acids in eukaryotes were largely ignored due to challenges in their genetic and biochemical detection. However, with the ever-increasing availability of completed genome sequences and deep sequencing, which allows analysis of genome-wide ribosome occupancy, hundreds of small proteins are now being identified. This brings to the forefront the challenges and opportunities associated with the characterization of these proteins.See research article: http://www.biomedcentral.com/1471-2164/15/946.     

A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions

This article is a response to Wang and Luo. See correspondence article http://www.biomedcentral.com/1741-7007/10/30/ [WEBCITE] and the original research article http://www.biomedcentral.com/1741-7007/9/24 [WEBCITE].     

Segmental structure in banded mongoose calls

In complex animal vocalizations, such as bird or whale song, a great variety of songs can be produced via rearrangements of a smaller set of 'syllables', known as 'phonological syntax' or 'phonocoding' However, food or alarm calls, which function as referential signals, were previously thought to lack such combinatorial structure. A new study of calls in the banded mongoose Mungos mungo provides the first evidence of phonocoding at the level of single calls. The first portion of the call provides cues to the identity of the caller, and the second part encodes its current activity. This provides the first example known in animals of something akin to the consonants and vowels of human speech.See research article http://www.biomedcentral.com/1741-7007/10/97     

Hsp90 depletion goes wild

Hsp90 reveals phenotypic variation in the laboratory, but is Hsp90 depletion important in the wild? Recent work from Chen and Wagner in BMC Evolutionary Biology has discovered a naturally occurring Drosophila allele that downregulates Hsp90, creating sensitivity to cryptic genetic variation. Laboratory studies suggest that the exact magnitude of Hsp90 downregulation is important. Extreme Hsp90 depletion might reactivate transposable elements and/or induce aneuploidy, in addition to revealing cryptic genetic variation.See research article http://wwww.biomedcentral.com/1471-2148/12/25     

On optimal control policy for probabilistic Boolean network: a state reduction approach

Background

Probabilistic Boolean Network (PBN) is a popular model for studying genetic regulatory networks. An important and practical problem is to find the optimal control policy for a PBN so as to avoid the network from entering into undesirable states. A number of research works have been done by using dynamic programming-based (DP) method. However, due to the high computational complexity of PBNs, DP method is computationally inefficient for a large size network. Therefore it is natural to seek for approximation methods.

Results

Inspired by the state reduction strategies, we consider using dynamic programming in conjunction with state reduction approach to reduce the computational cost of the DP method. Numerical examples are given to demonstrate both the effectiveness and the efficiency of our proposed method.

Conclusions

Finding the optimal control policy for PBNs is meaningful. The proposed problem has been shown to be ${\sum }_2^p\mathsf{\text{ - hard}}$. By taking state reduction approach into consideration, the proposed method can speed up the computational time in applying dynamic programming-based algorithm. In particular, the proposed method is effective for larger size networks.

     

Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?

Lateral gene transfer (LGT) is the transmission of genes, sometimes across species barriers, outwith the classic vertical inheritance from parent to offspring. LGT is recognized as an important phenomenon that has shaped the genomes and biology of prokaryotes. Whether LGT in eukaryotes is important and widespread remains controversial. A study in BMC Biology concludes that LGT in eukaryotes is neither continuous nor prevalent and suggests a rule of thumb for judging when apparent LGT may reflect contamination.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0315-9.     

The Rabs: A family at the root of metazoan evolution

This paper is a response to Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid, O: Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biology 2011, 9:24. See research article at http://www.biomedcentral.com/1741-7007/9/24     

Paternal care behaviors of Japanese giant salamander <Emphasis Type="Italic">Andrias japonicus</Emphasis> in natural populations

Parental care among salamanders is typically provided by females. A rare case of parental care by male salamanders appears to occur in Cryptobranchidae. Yet, paternal behaviors have rarely been reported from natural populations of any Cryptobranchid salamanders, and their adaptive significance is poorly understood. The present study aimed to examine paternal care behaviors in a fully aquatic Japanese giant salamander (Andrias japonicus) in situ. At the beginning of the summer breeding season, large males, called den-masters, occupy burrows along stream banks for breeding and nesting. We videotaped post-breeding behaviors of two den-masters that stayed with the eggs, one in a natural and the other in an artificial nest in natural streams. We identified three behaviors, tail fanning, agitating and egg eating, to be parental care. Tail fanning provides oxygenated water for the eggs. We found that the den-master in the artificial nest, where dissolved oxygen level was lower, displayed tail fanning more frequently. Agitating the eggs with its head and body likely prevents yolk adhesions. The den-masters selectively ate whiter eggs that appeared to be dead or infected with water mold. This behavior, which we termed hygienic filial cannibalism, likely prevents water mold from spreading over healthy eggs. Digital video images relating to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj01a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj02a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj03a and http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj04a.     

The scent of your enemy is my friend? The acquisition of large carnivore scent by a smaller carnivore

Scent marking is critical to intraspecific communication in many mammal species, but little is known regarding its role in communication among different species. We used 4 years of motion-triggered video to document the use of scent marking areas—termed “community scrapes”—by pumas (Puma concolor) (http://www.momo-p.com/showdetail-e.php?movieid=momo160812pc01a) and other carnivore species. We found that gray foxes (Urocyon cinereoargenteus) routinely rubbed their cheeks on puma scrapes (http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc01a), and tested a series of hypotheses to determine its function. We found that gray foxes selected puma scrapes over other objects, and cheek rubbing by foxes was also correlated with how recently a puma had visited the scrape, suggesting that foxes were intent upon accumulating fresh puma scent. Cheek rubbing by foxes was not correlated with their breeding season or with how recently another fox had visited the site. Finally we found a cascading pattern in the occurrence of pumas, coyotes (Canis latrans) and gray foxes at community scrapes, suggesting that gray foxes may use puma scent to deter predation. This is the first published study to find evidence of a subordinate species using the scent of a dominant species to communicate with heterospecifics. The behavioral cascade we found in scent marking patterns also suggests that scent marking could be a mechanism that impacts the distribution and abundance of species. Additional videos pertaining to this article include http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc02a, and http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc03a.     

Interspecific responses of wild African carnivores to odour of 3-mercapto-3-methylbutanol,a component of wildcat and leopard urine

The scent of 3-mercapto-3-methylbutanol (3-M-3-MB), a volatile component of leopard (Panthera pardus) and domestic cat (Felis silvestris catus) urine, released at about 10 ng/s from slow-release dispensers, elicited scent-marking from African civet (Civettictis civetta), small-spotted genet (Genetta genetta) and slender mongoose (Galerella sanguinea), as well as African wildcat (F. s. cafra). A female leopard was apparently repelled by the scent. The scent-marking and scent-rubbing by species other than African wildcats and leopards were unexpected and have important implications for the design of studies to investigate chemical communication between wild mammals and the use of camera traps to estimate animal numbers. Videos showing the behaviours referred to in this article are available at; http://www.momo-p.com/showdetail-e.php?movieid=momo161223fs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gg01a.     

Tackling thermosensation with multidimensional phenotyping

Ring species, in which two different forms coexist in one region while being connected by a long chain of interbreeding populations encircling a geographic barrier, provide clear demonstrations of the evolution of one species into two. Known ring species are rare, but now Monahan et al. propose an intriguing new approach to discovering them: focus first on geography to find potential barriers. See research article http://www.biomedcentral.com/1741-7007/10/20     

First record of the genus Gynecaptera Skorikov, 1935 (Hymenoptera: Bradynobaenidae: Apterogyninae) from Saudi Arabia,with description of a new species

In the present study, the genus Gynecaptera Skorikov, 1935 Skorikov, A. S. (1935): Zur Mutilliden-Fauna Zentralasiens. Trudy tadzhikskoi basy Akademii Nauk. SSSR, 5, 257–349 + 7 plates. [Google Scholar] is recorded from the Arabian Peninsula for the first time, with a nocturnal new species, G. arabica Soliman &; Gadallah, which has been collected from the Riyadh region in Saudi Arabia and which is described and illustrated.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:F7ACB779-3750-4DC6-B29B-B7F290E7C7B4     

Mating and aggressive behaviour of <Emphasis Type="Italic">Brachyrhaphis olomina</Emphasis> (Cyprinodontiformes: Poeciliidae)

Despite the increasing interest in the use of intromittent male genitalia and coercive mating behaviour in poeciliids, detailed studies of the mating behaviour of most species in this family are lacking. We describe here the mating and aggressive behaviours of Brachyrhaphis olomina, and correlate them with the condition of the female’s ovum and embryos (immature, mature and pregnant). B. olomina performed a wide range of aggressive (sidle spread, tail beating, coordinate) and mating behaviours (approximation, touch, lateral display, touch-lateral display). Some behaviours (e.g. tail beating) are shared with other poeciliids, but two sexual behaviours (touch and lateral display) and one aggressive (coordinate) behaviour may be unique to B. olomina and were not reported in a previous study. Differences in male behaviour when paired with a female with mature ovum (more mating displays, no agonistic movements) suggest that males detect the female’s reproductive condition from some distance. The distinctive nature of mating behaviour in B. olomina highlights the importance of studying different species to have a better understanding of the evolution of mating and aggressive behaviours in poeciliids. Digital video images related to the article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo01a, http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo02a and http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo03a.