Transoceanic drift and the domestication of African bottle gourds in the Americas

Bottle gourd (Lagenaria siceraria) was one of the first domesticated plants, and the only one with a global distribution during pre-Columbian times. Although native to Africa, bottle gourd was in use by humans in east Asia, possibly as early as 11,000 y ago (BP) and in the Americas by 10,000 BP. Despite its utilitarian importance to diverse human populations, it remains unresolved how the bottle gourd came to be so widely distributed, and in particular how and when it arrived in the New World. A previous study using ancient DNA concluded that Paleoindians transported already domesticated gourds to the Americas from Asia when colonizing the New World [Erickson et al. (2005) Proc Natl Acad Sci USA 102(51):18315–18320]. However, this scenario requires the propagation of tropical-adapted bottle gourds across the Arctic. Here, we isolate 86,000 base pairs of plastid DNA from a geographically broad sample of archaeological and living bottle gourds. In contrast to the earlier results, we find that all pre-Columbian bottle gourds are most closely related to African gourds, not Asian gourds. Ocean-current drift modeling shows that wild African gourds could have simply floated across the Atlantic during the Late Pleistocene. Once they arrived in the New World, naturalized gourd populations likely became established in the Neotropics via dispersal by megafaunal mammals. These wild populations were domesticated in several distinct New World locales, most likely near established centers of food crop domestication.In independent centers of plant domestication worldwide, distinct suites of food crops tend to emerge from native flora under human selection. An exception to this is the bottle gourd (Lagenaria siceraria, Cucurbitaceae), which is native to Africa, but was used by diverse human cultures not only in Africa, but also across Eurasia, the Pacific Islands, and the New World during pre-Columbian times (1–4). Although bottle gourd fruits are edible, they are used by humans mostly for other purposes, including as lightweight, durable containers, fishnet floats, and musical instruments (5). This variety of utilitarian applications likely explains why bottle gourds are so globally pervasive.In the New World, bottle gourds appear in archaeological contexts as early as 10,000 BP (6) (9). Bottle gourds were long proposed to have arrived in the Americas via long-range dispersal on ocean currents (10–13). However, an analysis of DNA from living and archaeological gourds suggested that the bottle gourd may have been transported into the New World by the first colonizing humans (6). In this scenario, the bottle gourd, like the dog (14), crossed the Bering Land Bridge with colonizing humans already in its domestic form, making the bottle gourd one of the earliest domesticated species (1, 6).

Table 1.

Archaeological samples and associated AMS radiocarbon dates for gourd rind fragments used in this study

Gregor Johann Mendel and Modern Evolutionary Biology: Molecular genetic variation of animals and plants under domestication

Domesticated plants and animals played crucial roles as models for evolutionary change by means of natural selection and for establishing the rules of inheritance, originally proposed by Charles Darwin and Gregor Mendel, respectively. Here, we review progress that has been made during the last 35 y in unraveling the molecular genetic variation underlying the stunning phenotypic diversity in crops and domesticated animals that inspired Mendel and Darwin. We notice that numerous domestication genes, crucial for the domestication process, have been identified in plants, whereas animal domestication appears to have a polygenic background with no obvious “domestication genes” involved. Although model organisms, such as Drosophila and Arabidopsis, have replaced domesticated species as models for basic research, the latter are still outstanding models for evolutionary research because phenotypic change in these species represents an evolutionary process over thousands of years. A consequence of this is that some alleles contributing to phenotypic diversity have evolved by accumulating multiple changes in the same gene. The continued molecular characterization of crops and farm animals with ever sharper tools is essential for future food security.     

From the Cover: Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal

Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (∼2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (∼1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ∼800 y ago.

Early archaeological and genomic evidence from Zhokhov Island in Arctic Siberia indicates that dogs belonging to a distinct lineage were an essential component of life in the Arctic for over 9,500 y (1, 2). This tight link between people and dogs continues in Siberian communities such as the Koryaks, Itel’mens, Chukchi, and Nenets, where dogs continued to be used for hunting, herding, and sledding among other activities (3–5). Recent genomic data obtained from Samoyedic-speaking communities such as Nenets and Selkups suggest that during the Holocene they received limited gene flow from neighboring groups, including Steppe pastoralists (6, 7). Given that humans and their dogs often migrate and interact in parallel (8), it is possible that Siberian dogs also experienced limited gene flow from other populations.In contrast to the human genomic evidence, linguistic and ethnographic data suggest more dynamic processes. Specifically, these data suggest that Samoyedic-speaking peoples of Northwest Siberia migrated from southern Siberia, or neighboring regions of southeast Europe, to the Arctic as recently as ∼3,000 to 4,000 y ago (9–12). In addition, archaeological sites such as Ust’-Polui in Northwest Siberia show evidence of iron and bronze metallurgy and isolated finds such as glass beads that were likely introduced from the Steppe, Black Sea, or the Near East (13–15). The presence of this material culture suggests that these communities participated in broad-ranging trade networks (13–15). The proposed migrations and exchanges of materials and practices potentially also involved dogs, which could have led to admixture, improvement, and ultimately to the establishment of modern Siberian dog lineages such as the modern Samoyed breed.To assess whether the Northwest Siberian Arctic dogs population was continuous, or was instead marked by admixture (possibly in relation to the influx of material culture from other parts of Eurasia), we sequenced 20 ancient and historical Siberian and Eurasian Steppe dogs ranging in age from 11,000 to 60 y ago and in genomic coverage between 0.1× and 11.1× (Dataset S1). We then analyzed these genomes alongside publicly available ancient (n = 29) and modern (n = 120) canids (Fig. 1A and Dataset S2).Open in a separate windowFig. 1.(A) Map of ancient dogs included in the study with sample name and age (kya) with an Inset map of the Iamal-Nenets region of Northwest Siberia. Data from samples represented by circles were generated in this study with a mean genome coverage between 0.1 and 19.9×; triangles represent publicly available ancient dogs. The colors of the data points represent the D-statistic value of the form D (black jackal, sample; Zhokhov, ASHQ01). Red-shifted colors show a closer affinity to ASHQ01 (ancient Near Eastern dog), and blue-shifted colors indicate a closer affinity to Zhokhov (ancient Arctic dog). (B) A TreeMix phylogeny with five migration edges that are indicated by gray dotted lines. Each population contains between one and three individuals (SI Appendix, Table S1). The color of the branches correspond to average D-statistic value in A. Complete models with the outgroup and edge weights, as well as models with additional edges can be found in SI Appendix, Fig. S3.     

From the Cover: PNAS Plus: Prehistoric genomes reveal the genetic foundation and cost of horse domestication

The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski’s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the “cost of domestication” hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.The domestication of the horse had a far-reaching impact on the sociopolitical and economic trajectories of human societies (1). It not only provided meat and milk (2) but also enabled the development of continent-sized nomadic empires, by transforming warfare and allowing for the rapid spread of goods and information over long distances. However, despite the characterization of the genome of modern horses (3), an understanding of the genetic processes underlying horse domestication is still lacking. In other organisms, such an understanding is usually achieved by comparing the genomes of domesticated species and their wild relatives (4–6), but this approach is not directly applicable to horses. Recent genome-wide analyses have shown that Przewalski’s horse, the last truly wild horse population remaining today, is not the direct ancestor of domesticated horses (7, 8). Instead, it likely represents a sister population that separated from the ancestral population of domesticated horses some 38–72 kya (9). This date significantly predates not only the widely accepted date for the beginning of horse domestication, ca. 5.5 kya (2), but also the earliest potential evidence for horse domestication, ca. 7.5 kya (10). In addition, the current Przewalski’s horse population descends from a captive stock consisting of only 13 founder individuals (7). This severe demographic bottleneck, together with inbreeding resulting from unequal contributions from different captive lineages, likely caused a substantial loss of the diversity once present in Przewalski’s horses. As a result, no modern horse population can fully represent the genetic diversity ancestral to the modern, domesticated gene pool (11–13).Ancient DNA allows tracking of past population histories through time, accessing the gene pools of wild animals predating domestication and exploring genetic variation that has been lost in extant populations. Recovery of ancient DNA, coupled with low-throughput gene candidate analyses, has previously been used to investigate changes in the genetic diversity of horses over time. This approach revealed coat color variation as one early result of domestication, by showing that the selection of multiple alleles driving diverse coloration patterns was already ongoing in the Early Bronze Age (14). It has also revealed a loss of Y-chromosomal haplotypes on both the Przewalski’s and domestic horse lineages (12).Using next-generation sequencing, the complete genome sequence of ancient individuals can now be deciphered (15), with qualities rivaling the qualities of modern genomes (16–18). We characterized complete genome sequences of two ancient horse specimens predating the earliest evidence of horse domestication to reveal the population context in which horse domestication took place. We compared the genomic information of these specimens with genomic information of six domestic horses, representing five breeds, and one Przewalski’s horse (9), ranging from a 7.4- to 32.7-fold average depth of coverage. We also included the domestic donkey as an outgroup, which represents a sister lineage of modern horses and shares a most common recent ancestor with horses 4.0–4.5 Mya ago (9). This comparison enabled us to reconstruct the relationships between wild and domesticated horses, and to explore the genetic mechanisms underlying the behavioral, physiological, and other biological changes that accompanied horse domestication.     

From the Cover: Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains

The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.

The initial domestication of southwest Asian crops and livestock species unfolded across the Fertile Crescent after the end of the Younger Dryas climatic downturn circa 9600 BC and coalesced into fully integrated agricultural economies by 7500 cal BC (1). Until recently, the western part of this region was cast as the epicenter of this transition, while the Zagros Mountains, at the eastern end of the Fertile Crescent, was considered a backwater, slow to receive and embrace domesticates and food-producing technologies from farther west (2, 3). However, this region of western Iran has been recently postulated as a primary center for the domestication of a number of plant and animal species (4), including barley (5, 6), possibly emmer wheat (7), several pulse species (8), and most notably, goats (9). This latter hypothesis has been supported by ancient genomic data, which indicate that the eastern Fertile Crescent was one of three regions key in shaping the Neolithic goat gene pool (10).Here we explore the transition from the hunting of wild bezoar goats (Capra aegagrus) to their initial management and subsequent domestication in the eastern Fertile Crescent by combining ancient genome sequencing and archaeozoological evidence from Ganj Dareh and Tepe Abdul Hosein, two sites in the central Zagros dating to the early or Aceramic Neolithic (AN) circa 8000 cal BC. These genomic data present a singular opportunity to deepen our understanding of the consequences of goat management at the dawn of domestication.     

换代犬与阻断结膜吸吮线虫病流行关系的研究

冒的为了探寻控制结膜吸吮线虫病流行的有效措施。方法采取对现症病人所在村的传染源犬、传播媒介冈田氏饶眼果蝇(A.o)感染结膜吸吮线虫(T.c)进行调查和实行换代犬后的犬及A.o感染T.c追踪调查,将前后调查结果进行比较。结果 1981～1992年安徽淮北地区连续出现T.c病人,这时对宿县芦岭、泗县大庄、五河县城郊病人所在村犬进行了检查,当时感染T.c分别占63.6％(14/22)、75.0％(12/16)和86.1％(19/231)。同时重点检查了五河城郊A.o蝇737只,阳性12只,其感染率为1.6％。其中个别A.o带有T.c感染期幼虫达20余条。于1998年即实行换代犬之后 5年,再查五河城郊及泗县大庄家犬计31只,全部阴性。此期间无新病例。同时查五河城郊A.o果蝇206只,也全部阴性。表明换代犬已失去原先犬群那种强力传染源作用。于 1998～1999年在合肥郊区一新病例居住村,对犬进行检查,犬感染T.c占79.2％(19/24),查犬时即取出虫体,为犬治病。此时进行健康教育,群众易于接受,采用换代大及拴养犬措施,预防该病。于2000年再去检查该村犬12只,阳性8只,占66.7％,犬的感染率及感染度虽较前2年有所降低,但其传染源作用的下降,明显不如其他实行群众性换代犬措施地区的效果好。结论对结膜吸吮线虫病流行区,在健康教育基础上,果断实行换代大措施,是阻断本病传播的最有效方法。     

犬Marshall韧带的电生理学特点及其形态结构观察

目的 :观察 Marshall韧带 （L OM）的电生理学特点及其组织形态 ,探讨 L OM在局灶性房颤发病机制中的地位。方法 :选用健康犬 8只 ,放置心内电极导管和心外膜电极 ,同步记录高位右房 （HRA） ,左心耳 （L AA） ,L OM的电活动。射频消融 L OM靠近冠状窦的部位。比较消融前后 HRA- L AA间期 ,HRA- L AM（左房 ）间期 ,HRA- L OM间期 ,L AM- L OM间期。切取 L OM,进行组织学观察。结果 :窦性心律时 ,在 L OM上可以记录到双电位 ,前者是 L AM电位 ,后者是 L OM电位 ,消融 L OM靠近冠状窦的部位 ,L OM电位消失 ,消融前后 ,HRA- L AA间期、HRA- L AM间期对比无显著性差异 （P>0 .0 5 ）。组织切片显示 L OM内含有心肌组织 ,与深层左房肌被脂肪层隔离 ,脂肪层内含有大量的神经组织。结论 :L OM电位是 L OM内心肌组织产生的 ,L OM可能是局灶性房颤的起源部位之一。射频消融 L OM靠近冠状窦的部位对左右房间传导无影响。对起源于 L OM的局灶性房颤 ,消融这一部位可能有效。     

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 dogs admitted to the Veterinary Teaching Hospital for any given reason. The second group included dogs that shared households with confirmed COVID-19 cases in humans. This study group numbered 78 dogs. In COVID-19 infected households, 43.9% tested ELISA positive, and neutralising antibodies were detected in 25.64% of dogs. Those data are comparable with the secondary attack rate in the human population. With 14.69% of dogs in the general population testing ELISA positive, there was a surge of SARS-CoV-2 infections within the dog population amid the second wave of the pandemic. Noticeably seroprevalence of SARS-CoV-2 in the dog and the human population did not differ at the end of the study period. Male sex, breed and age were identified as significant risk factors. This study gives strong evidence that while acute dog infections are mostly asymptomatic, they can pose a significant risk to dog health. Due to the retrospective nature of this study, samples for viral isolation and PCR were unavailable. Still, seropositive dogs had a 1.97 times greater risk for developing central nervous symptoms.     

The hemodynamic properties of amlodipine in anesthetised and conscious dogs: Comparison with nitrendipine and influence of beta-adrenergic blockade

Summary The hemodynamic actions of the new dihydropyridine calcium-channel blocker amlodipine were assessed and compared with those of nitrendipine using anesthetised dogs and were also investigated in conscious dogs with and without beta-adrenergic blockade. After bolus intravenous administration, amlodipine (25 to 1600 g/kg) or nitrendipine (1 to 128 g/kg) was administered to anesthetised dogs at 30-minute intervals, caused dose-related reductions in systemic and coronary vascular resistances with corresponding increases in cardiac output and coronary flow. Nitrendipine, unlike amlodipine, caused marked acute hypotension. The onset of action of amlodipine was markedly slower than that of nitrendipine, and effects were maintained for 30 minutes—recovery from nitrendipine was largely complete at 30 minutes. In conscious dogs, amlodipine (250, 500, 1000 g/kg IV) caused dose-related reductions in systemic vascular resistance that approached maximum within 5 minutes and persisted for over 4 hours. Reflex increases in heart rate, cardiac output, and cardiac contractility were attentuated by prior treatment with propranolol, resulting in earlier and greater falls in blood pressure, but no marked adverse effects on cardiac contraction or conduction. In the absence of propranolol, maximum falls in blood pressure occurred 3 to 4 hours after the dose, possibly as a result of the changed baroceptor sensitivity induced by amlodipine. These results show amlodipine to have the basic hemodynamic profile of other dihydropyridine calcium-channel blockers, but in addition it demonstrates a slower onset and longer duration of action; the reasons behind these pharmacodynamic properties are discussed.     

No evidence for linkage between hla and maturity onset type of diabetes in young people

Summary Studies with 20 different genetic marker systems were performed in a large kindred including 18 members affected with maturity onset type of diabetes of young people. Linkage closer than 0.1 could be excluded for ABO and Gm, and linkage closer than 0.05 for HLA GLO, and haptoglobin. No significant positive lod scores were found.     

Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation

In budding yeast, the MutL homolog heterodimer Mlh1-Mlh3 (MutLγ) plays a central role in the formation of meiotic crossovers. It is also involved in the repair of a subset of mismatches besides the main mismatch repair (MMR) endonuclease Mlh1-Pms1 (MutLα). The heterodimer interface and endonuclease sites of MutLγ and MutLα are located in their C-terminal domain (CTD). The molecular basis of MutLγ’s dual roles in MMR and meiosis is not known. To better understand the specificity of MutLγ, we characterized the crystal structure of Saccharomyces cerevisiae MutLγ(CTD). Although MutLγ(CTD) presents overall similarities with MutLα(CTD), it harbors some rearrangement of the surface surrounding the active site, which indicates altered substrate preference. The last amino acids of Mlh1 participate in the Mlh3 endonuclease site as previously reported for Pms1. We characterized mlh1 alleles and showed a critical role of this Mlh1 extreme C terminus both in MMR and in meiotic recombination. We showed that the MutLγ(CTD) preferentially binds Holliday junctions, contrary to MutLα(CTD). We characterized Mlh3 positions on the N-terminal domain (NTD) and CTD that could contribute to the positioning of the NTD close to the CTD in the context of the full-length MutLγ. Finally, crystal packing revealed an assembly of MutLγ(CTD) molecules in filament structures. Mutation at the corresponding interfaces reduced crossover formation, suggesting that these superstructures may contribute to the oligomer formation proposed for MutLγ. This study defines clear divergent features between the MutL homologs and identifies, at the molecular level, their specialization toward MMR or meiotic recombination functions.

During the first meiotic division, in most organisms, each pair of homologous chromosomes (homologs) needs to experience at least one crossover to ensure their accurate segregation and increase genetic diversity of the progeny (1, 2). Crossovers are generated after programmed DNA double-strand break (DSB) formation, and their subsequent repair by homologous recombination (3). Failure to achieve at least one crossover per homolog pair results in aneuploid gametes. These dysfunctions are frequent causes of spontaneous miscarriages and birth defects in humans (1). DSBs are generated by the meiosis-specific Spo11 protein and resected to form 3′ single-stranded tails that are directed to invade and pair with an unbroken homologous template, preferentially on the homolog (3). Invasion intermediates are a substrate for DNA synthesis. After the capture of the second DSB end, a subset of the intermediates is converted into double Holliday junctions (dHJs), which in meiosis are primarily resolved into crossovers (4, 5). The remaining recombination intermediates are repaired as noncrossovers.MutLγ (Mlh1-Mlh3 in yeast and MLH1-MLH3 in human) is essential for the formation of meiotic crossovers in many organisms. The MutLγ heterodimer possesses, similarly to MutLα (Mlh1-Pms1 in yeast, MLH1-PMS2 in human), a latent endonuclease activity (6–10). It has been proposed that the MutLγ endonuclease activity catalyzes the resolution of the dHJ intermediates and promotes the formation of crossovers (8, 11). In agreement with this, Mlh1 and Mlh3 form foci on pachytene chromosomes in different organisms at future crossover sites (12–14). In yeast mlh3 mutants, the crossover rates are reduced to 50 to 70% of the wild-type level (8, 15–17). These mutants exhibit failure in chromosome disjunction and consequently a decrease of spore viability. In Mlh3^-/- mice, males and females present a crossover defect that leads to aneuploidy (18). In agreement with the proposed resolvase role of MutLγ, a mutant of the active site within the conserved DQHAX₂EX₄E motif of Saccharomyces cerevisiae Mlh3, D523N, results in a loss of activity and confers a phenotype similar to the mlh3∆ mutant with decreased crossover frequencies (8). A mutation in the endonuclease domain of mouse MLH3 leads to infertile males and strongly reduced crossover numbers, despite a correct loading of factors essential for crossover resolution (19). In budding yeast and mammals, MLH1 deletion is also associated with severe dysfunctions in meiosis due to crossover defects, combined with high genetic instability due to its additional central role with Pms1 (as part of the MutLα complex) in mutation avoidance (20).In budding yeast, the majority of meiotic crossovers are formed by MutLγ, requiring in addition other proteins including the ZMM proteins (Zip1-4, Spo16, Mer3, and Msh4-Msh5), Exo1, and the Sgs1-Top3-Rmi1 complex (11, 21). The ZMM factors are proposed to stabilize the recombination intermediates and protect them from the action of helicases (reviewed in ref. 22). The 5′-3′ exonuclease, Exo1, is important for crossover formation independently of its nuclease activity and likely acts as scaffold factor in particular through its interaction motif with Mlh1 (17). We recently reported that MutLγ-Exo1 associates with recombination intermediates, followed by direct Cdc5 recruitment that triggers MutLγ crossover activity (23). Despite its central role in the formation of crossovers, to date, the MutLγ endonuclease does not show any specific activity on either a single HJ or dHJ DNA substrate in vitro, in contrast to other resolvases or structure-specific endonucleases (24). Recently, it was shown that human MutLγ is part of an ensemble with MutSγ, EXO1, RFC, and PCNA that preferentially cleaves plasmid DNA containing a HJ, although it does not cleave symmetrically across the junction, as would be expected for a canonical resolvase (25, 26).MutLγ is also an accessory factor of the postreplicative mismatch repair (MMR). In S. cerevisiae, MutLα is the major MutL homolog involved in MMR. It is targeted to DNA mismatches by the MutS homologs and introduces DNA nicks to initiate the excision of the strand containing the mismatch. MutLα contains an endonuclease site formed by three conserved motifs in Pms1 and the last conserved amino acids of Mlh1 (6, 7, 27). Mutation of this active site (e.g., pms1E707K in yeast) is associated with high mutations rates. A minor role of MutLγ has been reported in the repair of a subset of DNA mismatches recognized by Msh2-Msh3 (28, 29). The third MutL heterodimer, Mlh1-Mlh2 (MLH1-PMS1 in mammals) or MutLβ, has no endonuclease motif or activity. In yeast, mlh2Δ cells present only a slight defect in the repair of a subset of frameshift mutations (30–32). Apart from this function in MMR, we recently identified an interaction of MutLβ with Mer3 helicase that limits gene conversion tract lengths (31). A major challenge is to further characterize the molecular basis of the specific interactions and regulations of the three MutL homologs with their DNA substrates and protein partners in MMR and in meiotic recombination.MutLγ and MutLα present an overall common organization with a N-terminal domain (NTD) bearing an ATPase function, connected through a long linker to a C-terminal domain (CTD). The CTD mediates the dimerization of the complexes (33, 34) and possesses the endonuclease site (6–8). Upon ADP and ATP binding, the NTD undergoes large asymmetric conformational changes that can position it into a close proximity to the CTD (35, 36). The heterodimers MutLα and MutLγ can slide on double-stranded DNA (dsDNA) with linear diffusion modes (37, 38) and control strand excision during MMR (39). However, both heterodimers differ in their DNA-binding properties. MutLα has very low affinity for short dsDNA in physiological salt concentrations and can bind cooperatively to long dsDNA (>200 bp), forming long continuous protein tracts (40). In contrast, MutLγ binds short-branched DNA substrates with a higher affinity (in the nanomolar range) and with a marked preference for HJs (9). MutLγ also binds, albeit more weakly, short and long dsDNA and is proposed to form oligomers on long dsDNA (9, 41). The Pms1 and Mlh3 subunits present a moderate sequence identity precluding correct modeling of MutLγ from the MutLα crystal structures and thus limiting our understanding of the molecular basis of the specificity of MutLα and MutLγ heterodimers in MMR and meiosis, respectively.Here, we present the crystal structure of the S. cerevisiae MutLγ(CTD), and we compare it with the three-dimensional structure of the S. cerevisiae MutLα(CTD) that we previously reported (27). We reveal differences between the two complexes with regard to the size of the heterodimerization interface, the regulatory domain position, and the shape of the cavity surrounding the endonuclease site. We characterize the role of the last amino acids of Mlh1 using mutant alleles and identify a central role of the last three conserved residues of Mlh1 in vivo for both MMR and meiotic recombination. We analyze the DNA-binding specificities of the MutLα(CTD) and Mut-Lγ(CTD) and compare to the properties of full-length proteins. We then identify positions in Mlh3(NTD) and Mlh3(CTD) that can participate to the positioning of the NTD close to the CTD and characterize the corresponding mutants in meiosis. Finally, we report a filament arrangement of the MutLγ(CTD) in the crystal in agreement with oligomers proposed in previous studies (25, 41), and we characterize an allele mutated in this oligomerization region.     

From the Cover: Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

As an economic crop, pepper satisfies people’s spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.Pepper (Capsicum) is an economically important genus of the Solanaceae family, which also includes tomato and potato. The genus includes at least 32 species native to tropical America (1), of which C. annuum L., C. baccatum L., C. chinense Jacq., C. frutescens L., and C. pubescens (Ruiz & Pavon) were domesticated as far back as 6000 B.C. by Native Americans (2). Peppers have a wide diversity of fruit shape, size, and color. Pungent peppers are used as spices, and sweet peppers are used as vegetables. After the return of Columbus from America in 1492 and subsequent voyages of exploration, peppers spread around the world because of adaptation to different agroclimatic regions and rapid adoption of pepper in different cultures as food, medicine, and ornamentals (3, 4). Pepper global production in 2011 reached 34.6 million tons fresh fruit and 3.5 million tons dried pods harvested in 3.9 million hectares (www.fao.org). Despite the growing commercial importance of pepper, the molecular mechanisms that modulate fruit size, shape, and yield are mostly unknown.Since the 1990s, genetic diversity and allelic shifts among cultivars, domesticated landraces, and wild accessions have been partially explored using restricted sets of anonymous or neutral molecular markers (5–9) and annotated DNA sequences (10). These studies reported that the genetic variability among sweet and large-fruited C. annuum cultivars was very restricted and suggested that changes in the allelic frequencies and a subsequent loss of diversity during the transition from wild to cultivated populations occurred even in areas of species cohabitation. The relatively low levels of genetic diversity in the primary gene pool have constrained pepper genetic improvement. Another primary reason for limited applied and basic research in pepper has been lack of a reference genome sequence of ∼3.3 Gb (11). Recent work comparing two members of the Solanaceae family (pepper and tomato) has begun to shed light on the processes that influence the dynamics of genome size in angiosperms (12, 13).To contribute to the understanding of pepper biology and evolution and accelerate agricultural applications, we generated and analyzed two reference genome sequences of cultivated Zunla-1 and wild Chiltepin (2n = 2x = 24). The two pepper genomes together with 20 resequencing accessions, including 3 accessions that are classified as semiwild/wild, provide a better understanding of the evolution, domestication, and divergence of various pepper species and ultimately, will enhance future genetic improvement of this important worldwide crop.     

Archaeological and genetic insights into the origins of domesticated rice

Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world’s population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.     

The relationship between peripheral glucose utilisation and insulin sensitivity in the regulation of hepatic glucose production: studies in normal and alloxan-diabetic dogs

BACKGROUND: Hepatic glucose overproduction (HGP) of diabetes could be primary or could occur in response to the metabolic needs of peripheral (skeletal muscle (SkM)) tissues. This question was tested in normal and diabetic dogs. METHODS: HGP, SkM glucose uptake (Rd(tissue)), metabolic clearance of glucose (MCRg) and glycolytic flux (GF(exog)), and SkM biopsies were measured in the same dogs before and after alloxan-induced diabetes. Normal dogs were exposed to (1) an extended 20-h fast, (2) low- and high-dose glucose infusions (GINF) at basal insulinaemia, and chronic diabetic dogs were exposed to (3) hyperglycaemia, (4) phlorizin-induced normoglycaemia, and (5) poor and good diabetic control. RESULTS: (1) Prolonged fast: HGP, Rd(tissue), and GF(exog) fell in parallel (p < 0.05). (2) Low-dose GINF: plasma glucose, insulin, Rd(tissue), MCRg, and GF(exog) were unchanged, but HGP fell by approximately 40%, paralleling the supplemental GINF. (3) High-dose GINF at basal insulin: plasma glucose doubled and synchronous changes in HGP, Rd(tissue), MCRg, and GF(exog) occurred; IC(glucose), G6P, and glycogen were unchanged. (4) Hyperglycaemic diabetes: HGP was raised (p < 0.05), matching urinary glucose loss (UGL) and decreased MCR(g), and maintaining normal basal Rd(tissue) and GF(exog). SkM IC(glucose) was increased and glycogen decreased (both p < 0.05). (5) Phlorizin-induced normoglycaemia in diabetic dogs: HGP rose, matching the increased UGL, while maintaining normal Rd(tissue) and GF(exog). Intramuscular substrates normalised. (6) Whole body and SkM metabolism normalised with correction of the insulin resistance and good diabetic control. CONCLUSION: HGP reflects whether SkM is in a state of relative glucose 'excess' or absolute/relative glucose 'deprivation'.     

Insights into the multifactorial causation of obesity by integrated genetic and epigenetic analysis

Obesity is a highly heritable multifactorial disease that places an enormous burden on human health. Its increasing prevalence and the concomitant‐reduced life expectancy has intensified the search for new analytical methods that can reduce the knowledge gap between genetic susceptibility and functional consequences of the disease pathology. Although the influence of genetics and epigenetics has been studied independently in the past, there is increasing evidence that genetic variants interact with environmental factors through epigenetic regulation. This suggests that a combined analysis of genetic and epigenetic variation may be more effective in characterizing the obesity phenotype. To date, limited genome‐wide integrative analyses have been performed. In this review, we provide an overview of the latest findings, advantages, and challenges and discuss future perspectives.     

Ultrastructure of a coronary chemoreceptor of dogs and cats

Ultrastructure of a coronary chemoreceptor which causes a hypertensive reflex was examined in three normal dogs and three normal cats. The tissue is a periarterial glomoid body composed of highly vascular, grape-like clusters regularly located in the immediate vicinity of the left main coronary artery, from which it receives its blood supply. Its general histological organization resembles that of the carotid body. Morphometric analysis indicates that chief cells were about twice as numerous as sustentacular cells. The chief cells contain abundant osmiophilic dense granules and are surrounded by the processes of sustentacular cells. These dense granules resemble those of the carotid body and adrenal medulla, suggesting that they also may be involved in the production and storage of amines.Abundant nerve endings and formed synapses are associated with the chief cells. Numerous sympathetic and parasympathetic efferent nerve endings had characteristic presynaptic junctions to chief cells. In contrast the sensory afferents packed with mitochondria but with few synaptic vesicles had characteristic postsynaptic junctions to the chief cells. These findings suggest that the chief cells not only stores amines but also serves as a sensory or chemoreceptive site.     

Translating evidence into practice for people with osteoarthritis of the hip and knee

There is an international focus on improving the quality of care for people with chronic conditions, including those with chronic rheumatic conditions such as osteoarthritis (OA). A number of evidence-based clinical practice guidelines exist to guide clinician management of OA of the hip and knee. However, gaps and delays in the integration of these recommendations into practice still remain. This paper reviews the role of clinical practice guidelines within the contemporary discourse and practice of information translation. This discussion paper uses an OA quality improvement case study to illustrate how evidence for effective implementation strategies can be used in conjunction with a practical implementation model to plan and implement quality improvement projects. Dr. Brand received financial support from ILAR to present this paper at the APLAR conference in Kuala Lumpur, August 2006.