Re-examination of chimp protein kinases suggests "novel architectures" are gene prediction artifacts

<p>Abstract</p> <p>Background</p> <p>Anamika <it>et al</it><abbrgrp><abbr bid="B1">1</abbr></abbrgrp> recently published in this journal a sequence alignment analysis of protein kinases encoded by the chimpanzee genome in comparison to those in the human genome. From this analysis they concluded that several chimpanzee kinases have unusual domain arrangements.</p> <p>Results</p> <p>Re-examination of these kinases reveals claimed novel arrangements cannot withstand scrutiny; each is either not novel or represents over-analysis of weakly confident computer generated gene models. Additional sequence evidence available at the time of the paper's submission either directly contradict the gene models or suggest alternate gene models. These alternate models would minimize or eliminate the observed differences between human and chimp kinases.</p> <p>Conclusion</p> <p>None of the proposed novel chimpanzee kinase architectures are supported by experiment evidence. Guidelines to prevent such erroneous conclusions in similar papers are proposed.</p

An Annotated Checklist of the Crayfishes (Decapoda: Cambaridae) of Arkansas

Prior to the present study, 56 species with 3 additional subspecies for a total of 59 different taxa of crayfishes were recognized from Arkansas. We add a single species (Carmel Crayfish, Fallicambarus schusteri) to that list, subtract a documented synonym (Procambarus ferrugenius = Procambarus liberorum), update the classification to better reflect recent phylogenetic insights, and provide an updated annotated checklist of the 59 crayfish taxa of presently known from the state. There are 8 endemic species in Arkansas, including the Bayou Bodcau Crayfish (Bouchardina robisoni), Boston Mountains Crayfish (Cambarus causeyi), Hell Creek Cave Crayfish (C. zophonastes), Jefferson County Crayfish (Creaserinus gilpini), Ouachita Burrowing Crayfish (Fallicambarus harpi), Slenderwrist Burrowing Crayfish (F. petilicarpus), Saline Burrowing Crayfish (F. strawni), and Redspotted Stream Crayfish (Faxonius acares). There are also 2 federally endangered species, the Benton County Cave Crayfish (Cambarus aculabrum) and the Hell Creek Cave Crayfish (C. zophonastes) that inhabit Arkansas karst habitat. We expect that additional species will be included in the list with further DNA analyses

A human systems integration approach to energy efficiency in ground transportation

This effort establishes the feasibility of implementing telematics systems into theUnited States Marine Corps’ decision-making process in order to increase its operational reach and overall effectiveness. It is based around a qualitative case study evaluation of commercially implemented telematics. Telematics, as defined by Fleetmatics, is the integrated use of telecommunications combined with information and technology communication systems used to achieve improved operational capabilities while creating a more effective and efficient workforce. This research was done through numerous interviews with a variety of personnel who use telematics. The information is then partitioned and analyzed using a systems engineering framework utilizing a human systems integration methodology. This analysis acts as a framework to outline best practices in metering and monitoring. Once established, it is applied to the Marine Corps to determine a feasible way to implement similar technologies on its ground vehicles. This study prescribes policies for the successful use of telematics systems in the Marine Corps that will make it a more fuel-efficient fighting force. As a result, the Marine Corps extends its operational reach, improves its warfighting capability, and reduces the risk to the warfighter.http://archive.org/details/ahumsystemsinteg1094547855Outstanding ThesisLieutenant, United States NavyApproved for public release; distribution is unlimited

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.United States. Office of Naval Research. Young Investigator Program (Grant N000140510656)National Science Foundation (U.S.) (Synthetic Biology Engineering Research Center. Grant EEC-0540879)MIT Faculty Start-up FundCodon Devices, Inc

Islands of ice: Influence of free-drifting Antarctic icebergs on pelagic marine ecosystems

Regional warming around West Antarctica, including the Antarctic Peninsula, is related to the retreat of glaciers that has resulted in significant ice mass loss in recent decades. We examined freedrifting icebergs in the Atlantic sector of the Southern Ocean in December 2005, aboard ARSV Laurence M. Gould, and in June 2008 and March/April 2009, aboard RVIB Nathaniel B. Palmer. Prior to these studies, little information was available about the effects of icebergs on the pelagic realm.Facultad de Ciencias Naturales y Muse

First Results from HaloSat – A CubeSat to Study the Hot Galactic Halo

HaloSat is the first CubeSat for astrophysics funded by NASA\u27s Science Mission Directorate and is designed to map soft X-ray oxygen line emission across the sky in order to constrain the mass and spatial distribution of hot gas in the Milky Way. HaloSat will help determine if hot halos with temperatures near a million degrees bound to galaxies make a significant contribution to the cosmological budget of the normal matter (baryons). HaloSat was deployed from the International Space Station in July 2018 and began routine science operations in October 2018. We describe the on-orbit performance including calibration of the X-ray detectors and initial scientific results including an observation of a halo field and an observation of solar wind charge exchange emission from the helium-focusing cone

Lineage Abundance Estimation for SARS-CoV-2 in Wastewater Using Transcriptome Quantification Techniques

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable

Plated Cambrian Bilaterians Reveal the Earliest Stages of Echinoderm Evolution

Echinoderms are unique in being pentaradiate, having diverged from the ancestral bilaterian body plan more radically than any other animal phylum. This transformation arises during ontogeny, as echinoderm larvae are initially bilateral, then pass through an asymmetric phase, before giving rise to the pentaradiate adult. Many fossil echinoderms are radial and a few are asymmetric, but until now none have been described that show the original bilaterian stage in echinoderm evolution. Here we report new fossils from the early middle Cambrian of southern Europe that are the first echinoderms with a fully bilaterian body plan as adults. Morphologically they are intermediate between two of the most basal classes, the Ctenocystoidea and Cincta. This provides a root for all echinoderms and confirms that the earliest members were deposit feeders not suspension feeders