Rooting the eutherian tree: the power and pitfalls of phylogenomics

In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different genes reduced the bias

Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes

SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising ∼4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel SINE family, Sauria SINEs, whose members are widely distributed among genomes of lizards, snakes, and tuataras. Sauria SINEs comprise a 5′ tRNA-related region, a tRNA-unrelated region, and a 3′ tail region (containing short tandem repeats) derived from LINEs. We distinguished eight Sauria SINE subfamilies in genomes of four major squamate lineages and investigated their evolutionary relationships. Our data illustrate the overall efficacy of Sauria SINEs as novel retrotransposable markers for elucidation of squamate evolutionary history. We show that all Sauria SINEs share an identical 3′ sequence with Bov-B LINEs and propose that they utilize the enzymatic machinery of Bov-B LINEs for their own retrotransposition. This finding, along with the ubiquity of Bov-B LINEs previously demonstrated in squamate genomes, suggests that these LINEs have been an active partner of Sauria SINEs since this SINE family was generated more than 200 million years ago. © Springer-Verlag New York, LLC 2004

Single-incision laparoscopic-assisted surgery for colon cancer via a periumbilical approach using a surgical glove: Initial experience with 9 cases

AbstractOur initial experience of performing a single-incision laparoscopic-assisted (SILS) colectomy using a “home-made” multichannel port system is presented. Nine patients (5 women) with a median age of 67 years (range, 55–72 years) and a median body mass index of 21.2kg/m2 (range, 17.8–26.7kg/m2) underwent the SILS colectomy for colon cancer between September 2009 and March 2010. The sites of the primary tumor were the ascending colon (n=2), hepatic flexure (n=1), transverse colon (n=2), and sigmoid colon (n=4). Each trocar was introduced intraperitoneally through each finger of a surgical glove attached to the wound protector, which was applied to a midline fasciotomy made via a ¾-circular periumbilical incision. If necessary, one to three radial splits were added to the incision. The colon was mobilized intracorporeally, and the vessels were ligated intra- or extracorporeally. All the patients underwent a curative segmental colectomy without conversion to a standard multiport laparoscopy or open surgery. The median operative time and blood loss were 140min (range, 135–165min) and 50mL (range, 20–225mL), respectively. The median number of harvested lymph nodes was 18 (range, 6–31). The pathological stages included stage 0 (n=2), stage I (n=6), and stage III (n=1). The median number of postoperative analgesic use was one (range, 0–6). No intra- or postoperative complications occurred in this series. Our SILS colectomy procedure seems feasible and safe in selected patients with colon cancer

Theory of Acceleration of Decision Making by Correlated Time Sequences

Photonic accelerators have been intensively studied to provide enhanced information processing capability to benefit from the unique attributes of physical processes. Recently, it has been reported that chaotically oscillating ultrafast time series from a laser, called laser chaos, provide the ability to solve multi-armed bandit (MAB) problems or decision-making problems at GHz order. Furthermore, it has been confirmed that the negatively correlated time-domain structure of laser chaos contributes to the acceleration of decision-making. However, the underlying mechanism of why decision-making is accelerated by correlated time series is unknown. In this study, we demonstrate a theoretical model to account for accelerating decision-making by correlated time sequence. We first confirm the effectiveness of the negative autocorrelation inherent in time series for solving two-armed bandit problems using Fourier transform surrogate methods. We propose a theoretical model that concerns the correlated time series subjected to the decision-making system and the internal status of the system therein in a unified manner, inspired by correlated random walks. We demonstrate that the performance derived analytically by the theory agrees well with the numerical simulations, which confirms the validity of the proposed model and leads to optimal system design. The present study paves the way for improving the effectiveness of correlated time series for decision-making, impacting artificial intelligence and other applications

Distal gastrectomy via minilaparotomy for non-overweight patients with T1N0-1 gastric cancer: Initial experience of 30 cases

AbstractMinilaparotomy is considered to be a useful treatment alternative to laparoscopic-assisted surgery from the viewpoint of minimal invasiveness, although it has several limitations for the resection of malignant tumors. We evaluated the usefulness of distal gastrectomy via minilaparotomy for non-overweight patients with clinically diagnosed T1N0-1 gastric cancer. Clinicopathological and surgical data on 30 patients attempted to undergo distal gastrectomy via minilaparotomy (skin incision, ≤7cm) without laparoscopic assistance were analyzed. Inclusion criteria were clinically (preoperatively) diagnosed T1N0-1 gastric cancer that was not suitable for endoscopic mucosal resection located in the middle- or lower-third of the stomach and the patient body mass index ≤ 25.0 kg/m2. The minilaparotomy approach was successful in 27 patients (90%), while laparoscopic assistance was required to accomplish the procedures in three patients (10%). The type of lymph node dissection was D1 + α in 23 patients and D1 + β in 7 patients. The duration of surgery was 105–170 min (median, 143.5 min) and blood loss was 25–520 mL (median, 152.5 mL). Pathological stage was stage IA in 26 patients, IB in two patients, and stage II in two patients. Postoperative complications were wound infection in one patient, bleeding in one patient, and anastomotic ulcer in one patient. The length of postoperative stay was 7–41 (median, 11) days. With a median follow-up of 31 months, there was no recurrence. Distal gastrectomy via minilaparotomy seems feasible and safe in the majority of non-overweight patients with clinically diagnosed T1N0 gastric cancer

Age-dependent plasticity in the superior temporal sulcus in deaf humans: a functional MRI study

BACKGROUND: Sign-language comprehension activates the auditory cortex in deaf subjects. It is not known whether this functional plasticity in the temporal cortex is age dependent. We conducted functional magnetic-resonance imaging in six deaf signers who lost their hearing before the age of 2 years, five deaf signers who were >5 years of age at the time of hearing loss and six signers with normal hearing. The task was sentence comprehension in Japanese sign language. RESULTS: The sign-comprehension tasks activated the planum temporale of both early- and late-deaf subjects, but not that of hearing signers. In early-deaf subjects, the middle superior temporal sulcus was more prominently activated than in late-deaf subjects. CONCLUSIONS: As the middle superior temporal sulcus is known to respond selectively to human voices, our findings suggest that this subregion of the auditory-association cortex, when deprived of its proper input, might make a functional shift from human voice processing to visual processing in an age-dependent manner

Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate

Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an evolutionarily conserved genomic region named AS3_9 comprises three TEs (AmnSINE1, X6b_DNA and MER117), inserted side-by-side, and functions as a distal enhancer for wnt5a expression during morphogenesis of the mammalian secondary palate. Functional analysis of each TE revealed step-by-step retroposition/transposition and co-option together with acquisition of a binding site for Msx1 for its full enhancer function during mammalian evolution. The present study provides a new perspective suggesting that a huge variety of TEs, in combination, could have accelerated the diversity of cis-regulatory elements involved in morphological evolution

Cellular response of Parachlorella kessleri to a solid surface culture environment

Attached culture allows high biomass productivity and is a promising biomass cultivating system because neither a huge facility area nor a large volume of culture medium are needed. This study investigates photosynthetic and transcriptomic behaviors in Parachlorella kessleri cells on a solid surface after their transfer from liquid culture to elucidate the physiological and gene-expression regulatory mechanisms that underlie their vigorous proliferation. The chlorophyll content shows a decrease at 12 h after the transfer; however, it has fully recovered at 24 h, suggesting temporary decreases in the amounts of light harvesting complexes. On PAM analysis, it is demonstrated that the effective quantum yield of PSII decreases at 0 h right after the transfer, followed by its recovery in the next 24 h. A similar changing pattern is observed for the photochemical quenching, with the PSII maximum quantum yield remaining at an almost unaltered level. Non-photochemical quenching was increased at both 0 h and 12 h after the transfer. These observations suggest that electron transfer downstream of PSII but not PSII itself is only temporarily damaged in solid-surface cells just after the transfer, with light energy in excess being dissipated as heat for PSII protection. It thus seems that the photosynthetic machinery acclimates to high-light and/or dehydration stresses through its temporal size-down and functional regulation that start right after the transfer. Meanwhile, transcriptomic analysis by RNA-Seq demonstrates temporary upregulation at 12 h after the transfer as to the expression levels of many genes for photosynthesis, amino acid synthesis, general stress response, and ribosomal subunit proteins. These findings suggest that cells transferred to a solid surface become stressed immediately after transfer but can recover their high photosynthetic activity through adaptation of photosynthetic machinery and metabolic flow as well as induction of general stress response mechanisms within 24 h