Haplotype phasing: existing methods and new developments

Determination of haplotype phase is becoming increasingly important as we enter the era of large-scale sequencing because many of its applications, such as imputing low-frequency variants and characterizing the relationship between genetic variation and disease susceptibility, are particularly relevant to sequence data. Haplotype phase can be generated through laboratory-based experimental methods, or it can be estimated using computational approaches. We assess the haplotype phasing methods that are available, focusing in particular on statistical methods, and we discuss the practical aspects of their application. We also describe recent developments that may transform this field, particularly the use of identity-by-descent for computational phasing.     

Molecular epidemiology of TB: challenging dogmas and asking new questions

Traditional epidemiological methods provide insight into the dynamics of diseases such as tuberculosis. These traditional techniques have limitations and rely on a number of assumptions. The application of molecular techniques to the study of epidemiology has allowed us to gain new insights into the biology of the organism Mycobacterium tuberculosis and the dynamics of the disease. We have been enabled to push the limits of understanding of the epidemiology of this disease, allowing us to challenge the old clinical dogmas, ask new questions, design new strategies, and measure the efficacy of such new interventions to combat this age-old scourge. Among the dogmas challenged are that infection outside the home is commonplace, so-called relapse cases may in fact be largely reinfection, and active transmission may be more common than previously thought and reactivation disease relatively uncommon. These findings alone demand urgent attention and the design of optimal intervention strategies to reduce the burden of disease.     

Breaking the ties that bind: new advances in centrosome biology

The centrosome, which consists of two centrioles and the surrounding pericentriolar material, is the primary microtubule-organizing center (MTOC) in animal cells. Like chromosomes, centrosomes duplicate once per cell cycle and defects that lead to abnormalities in the number of centrosomes result in genomic instability, a hallmark of most cancer cells. Increasing evidence suggests that the separation of the two centrioles (disengagement) is required for centrosome duplication. After centriole disengagement, a proteinaceous linker is established that still connects the two centrioles. In G2, this linker is resolved (centrosome separation), thereby allowing the centrosomes to separate and form the poles of the bipolar spindle. Recent work has identified new players that regulate these two processes and revealed unexpected mechanisms controlling the centrosome cycle.     

Assimilation of new founders into existing captive populations

When new founders are added to an existing captive population, it is useful to establish a target number of offspring from each of these new founders that will maximize the amount of gene diversity retained in the captive population. This article presents a method for calculating an optimal number of offspring that should be produced from each new founder by considering the retention of founder genomes from dead and non-reproductive founders. © 1994 Wiley-Liss, Inc.     

Breaking the Q-cycle: finding new ways to study Qo through thermodynamic manipulations

Thirty years ago, Peter Mitchell won the Nobel Prize for proposing how electrical and proton gradients across bioenergetic membranes were the energy coupling intermediate between photosynthetic and respiratory electron transfer and cellular activities that include ATP production. A high point of his thinking was the development of the Q-cycle model that advanced our understanding of cytochrome bc ₁. While the principle tenets of his Q-cycle still hold true today, Mitchell did not explain the specific mechanism that allows the Qo site to perform this Q-cycle efficiently without undue energy loss. Though much speculation on Qo site mode of molecular action and regulation has been introduced over the 30 years after Mitchell collected his Prize, no single mechanism has been universally accepted. The mystery behind the Qo site mechanism remains unsolved due to elusive kinetic intermediates during Qo site electron transfer that have not been detected spectroscopically. Therefore, to reveal the Qo mechanism, we must look beyond traditional steady-state experimental approaches by changing cytochrome bc ₁ thermodynamics and promoting otherwise transient Qo site redox states. Invited paper to special issue “Peter Mitchell 30th anniversary” for JBB.